Fish Transcriptome and Expression Database

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baseline

The research plan is for study of impact gene expression of adult hybrid fish

key word
- Baseline
publication
- nan
abstract
- nan

sample list

	sample id	sample name	tissue	strain	treatment	description
	SRR1573239	Ctenopharyngodon idellus	liver	nan	Model organism or animal sample for Ctenopharyngodon idellus	nan
	SRR1185917	Ctenopharyngodon idellus	liver	nan	Model organism or animal sample for Ctenopharyngodon idellus	nan

PRJNA328412:

The results in this study provides the valuable resource for better understanding of grass carp immune system and defense mechanisms. It will also facilitate future functional studies on grass carp immunogenetics, and gradually apply in breeding programs of grass carp.

key word
- Baseline; Grass carp; Spleen; Transcriptome; Immune-relevant genes; RNA-SEQ DATA; RAINBOW-TROUT; SNP DETECTION; TELEOST FISH; COMMON CARP; EXPRESSION; RECEPTOR; HOX11; INFECTION; SEQUENCE
publication
- Li G et al., "Transcriptome profiling of developing spleen tissue and discovery of immune-related genes in grass carp (Ctenopharyngodon idella)", Fish and Shellfish Immunology; 2017; 60: 400-410.
abstract
- Grass carp Ctenopharyngodon idella is an important freshwater aquaculture species. However, studies regarding transcriptomic profiling of developing spleen tissue in the grass carp are lacking. Here, the transcriptome sequencing from the spleen tissue of one-year-old (cis1) and three-year-old (cis3) grass carp was performed using Illumina paired-end sequencing technology. The de novo assemblies yielded 48,970 unigenes with average lengths of 1264.51 bp from the two libraries. The assembled unigenes were evaluated and functionally annotated by comparing with sequences in major public databases including Nr, COG, Swiss-Prot, KEGG, Pfam and GO. Comparative analysis of expression levels revealed that a total of 38,254 unigenes were expressed in both the cis1 and cis3 libraries, while 4356 unigenes were expressed only in the cis1 library, and 3312 unigenes were expressed only in the cis3 library. Meanwhile, 1782 unigenes (including 903 down-regulated and 879 up-regulated unigenes) were differentially expressed between the two developmental stages of the grass carp spleen. Based on GO and KEGG enrichment analysis, these differentially expressed genes widely participated in the regulation of immunity and response in the grass carp. Moreover, the main components of six immune-related pathways were identified, including complement and coagulation cascades, Toll-like receptor signaling, B-cell receptor signaling, T-cell receptor signaling, antigen processing and presentation, and chemokine signaling. Finally, two identified transcripts including TLR 8 and complement component C8 were validated for reliability by RT-PCR. Collectively, the results obtained in this study will provide a basis for the study of molecular mechanisms in grass carp spleen development.

sample list

	sample id	sample name	tissue	strain	treatment	description
	SRR3923892	Spleen_1_year	spleen	nan	Untreated	Spleen of 1 year old female grass carp
	SRR3923906	Spleen_3_year	spleen	nan	Untreated	Spleen of 3 years old female grass carp

PRJNA347298:

Here we present the transcriptome of grass carp lymphocytes that seperated from blood, and we aimed at finding some new immune relevent genes from grass carp blood

key word
- Baseline; lymphocytes; blood
publication
- nan
abstract
- Here we present the transcriptome of grass carp lymphocytes that seperated from blood, and we aimed at finding some new immune relevent genes from grass carp blood

sample list

sample id	sample name	tissue	strain	treatment	description
SRR5019496	gc_ConA	blood	nan	nan	Unknown
SRR5019497	gc_LPS	blood	nan	nan	Unknown
SRR5019498	gc_control	blood	nan	nan	Unknown

PRJNA481087:

Digging out neuropeptides in grass carp and investigating their functions

key word
- Baseline; Neuropeptides; Optic tectum; Telencephalon; Olfactory bulb; Hypothalamus; Pituitary; GONADOTROPIN-RELEASING-HORMONE; VASOACTIVE INTESTINAL POLYPEPTIDE; TROUT ONCORHYNCHUS-MYKISS; FALSE DISCOVERY RATE; FOOD-INTAKE; GENE-EXPRESSION; OPTIC TECTUM; NEUROPEPTIDE-Y; SCHIZOTHORAX-PRENANTI; MOLECULAR-CLONING
publication
- Ye, C. , et al. "Structure and function analysis of various brain subregions and pituitary in grass carp (Ctenopharyngodon idellus)." Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 33(2020):100653-.
abstract
- It has been generally acknowledged that environment could alter the morphology and functional differentiation of vertebrate brain. However, as the largest group of all vertebrates, studies about the structures and functions of various brain subregions in teleost are still scarce. In this study, using grass carp as a model, histology method and RNA-sequencing were recruited to examine the microstructure and transcript levels among different brain subregions and pituitary. Histological results showed that the grass carp brain was composed of six parts, including olfactory bulb, telencephalon, hypothalamus, optic tectum, cerebellum, and medulla oblongata. In addition, compared to elasmobranchs and non-teleost bony ray-finned fishes, grass carp lost the hypothalamo-hypophyseal portal system, instead the hypophysiotropic neurons were directly terminated in the pituitary cells. At the transcriptomic level, our results suggested that the olfactory bulb might be related to reproduction and immune function. The telencephalon was deemed to be involved in the regulation of appetite and reproduction. The optic tectum might play important roles in the vision system and feeding. The hypothalamus could regulate feeding, and reproduction process. The medulla oblongata was related with the auditory system. The pituitary seemed to play pivotal roles in energy metabolism, organ development and reproduction. Finally, the correlation analysis suggested that the hypothalamus and the telencephalon were highly related, and close anatomical connection and overlapping functions suggested that the telencephalon and hypothalamus might be the regulation center of feeding and reproduction among teleost brain. This study provided a global view of the microstructures and specific functions of various brain subregions and pituitary in teleost. These results will be very helpful for further study in the neuroendocrinology regulation of growth and reproduction in teleost brain pituitary axis.

sample list

sample id	sample name	tissue	strain	treatment	description
SRR7522645	Te_S13_L006	telencephalon	nan	primary telencephalon cell	telencephalon
SRR7522646	Pit_S7_L007	pituitary	nan	primary pituitary cell	pituitary
SRR7522647	Ot_S3_L007	optic tectum	nan	primary optic tectum cell	optic tectum
SRR7522648	Ob_S2_L007	olfactory bulb	nan	primary olfactory bulb cell	olfactory bulb
SRR7522649	Mo_S5_L007	medulla oblongata	nan	primary medulla oblongata cell	medulla oblongata
SRR7522650	Hy_S6_L007	hypothalamus	nan	primary hypothalamus cell	hypothalamus
SRR7522651	Cx_S4_L007	cerebellum	nan	primary cerebellum cell	cerebellum

PRJNA510861:

genome evolution of the allotetraploid common carp

key word
- Baseline; GENE-EXPRESSION; DIVERGENCE; DUPLICATION; DNA; IDENTIFICATION; SELECTION; REVEALS; FINDER; TOOL; 2R
publication
- Peng Xu et al., "The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio", nature communications, 2019; 10: 4625.
abstract
- Common carp (Cyprinus carpio) is an allotetraploid species derived from recent whole genome duplication and provides a model to study polyploid genome evolution in vertebrates. Here, we generate three chromosome-level reference genomes of C. carpio and compare to related diploid Cyprinid genomes. We identify a Barbinae lineage as potential diploid progenitor of C. carpio and then divide the allotetraploid genome into two subgenomes marked by a distinct genome similarity to the diploid progenitor. We estimate that the two diploid progenitors diverged around 23 Mya and merged around 12.4 Mya based on the divergence rates of homoeologous genes and transposable elements in two subgenomes. No extensive gene losses are observed in either subgenome. Instead, we find gene expression bias across surveyed tissues such that subgenome B is more dominant in homoeologous expression. CG methylation in promoter regions may play an important role in altering gene expression in allotetraploid C. carpio.

sample list

sample id	sample name	tissue	strain	treatment	description
SRR8380198	GC_kidney	kidney	nan	nan	GC_kidney
SRR8380199	GC_gill	gill	nan	nan	GC_gill
SRR8380202	GC_liver	liver	nan	nan	GC_liver
SRR8380203	GC_intestine	intestine	nan	nan	GC_intestine
SRR8380204	GC_brain	brain	nan	nan	GC_brain
SRR8380205	GC_muscle	muscle	nan	nan	GC_muscle
SRR8380206	GC_skin	skin	nan	nan	GC_skin
SRR8380207	GC_spleen	spleen	nan	nan	GC_spleen
SRR8380240	GC_head-kindey	head-kindey	nan	nan	GC_head-kindey
SRR8380241	GC_blood	blood	nan	nan	GC_blood
SRR8380242	GC_heart	heart	nan	nan	GC_heart
SRR8380243	GC_sex	sex	nan	nan	GC_sex

PRJNA533182:

The grass carp B cell RNA-seq data for different subpopulation

key word
- Baseline; B cells
publication
- nan
abstract
- nan

sample list

sample id	sample name	tissue	strain	treatment	description
SRR8920833	Large_IgM_cells_2	head kidney	nan	large IgM B cell RNA-seq data from fish 2	Large_IgM_cells_2
SRR8920834	Small_IgM_cells_2	head kidney	nan	small IgM B cell RNA-seq data from fish 2	Small_IgM_cells_2
SRR8920836	Large_IgM_cells_1	head kidney	nan	large IgM B cell RNA-seq data from fish 1	Large_IgM_cells_1
SRR8920837	Small_IgM_cells_3	head kidney	nan	small IgM B cell RNA-seq data from fish 3	Small_IgM_cells_3
SRR8920832	Large_IgM_cells_3	head kidney	nan	large IgM B cell RNA-seq data from fish 3	Large_IgM_cells_3
SRR8920835	Small_IgM_cells_1	head kidney	nan	small IgM B cell RNA-seq data from fish 1	Small_IgM_cells_1

PRJCA010000:

Grass carp development

key word
- baseline; grass carp; development; zygotic activation; single-molecule real-time RNA sequencing; retained intron; LncRNA; messenger-RNA; transposable elements; noncoding regions; intron retention; gene; annotation; genome; tools; identification; mechanisms
publication
- Duan, Y et al. "Dynamic Transcriptional Landscape of Grass Carp (Ctenopharyngodon idella) Reveals Key Transcriptional Features Involved in Fish Development." INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)
abstract
- A high-quality baseline transcriptome is a valuable resource for developmental research as well as a useful reference for other studies. We gathered 41 samples representing 11 tissues/organs from 22 important developmental time points within 197 days of fertilization of grass carp eggs in order to systematically examine the role of lncRNAs and alternative splicing in fish development. We created a high-quality grass carp baseline transcriptome with a completeness of up to 93.98 percent by combining strand-specific RNA sequencing and single-molecule real-time RNA sequencing technologies, and we obtained temporal expression profiles of 33,055 genes and 77,582 transcripts during development and tissue differentiation. A family of short interspersed elements was preferentially expressed at the early stage of zygotic activation in grass carp, and its possible regulatory components were discovered through analysis. Additionally, after thoroughly analyzing alternative splicing events, we discovered that retained intron (RI) alternative splicing events change significantly in both zygotic activation and tissue differentiation. During zygotic activation, we also revealed the precise regulatory characteristics of the underlying functional RI events.

sample list

sample id	sample name	tissue	strain	treatment	description
CRR556658	T2	Ovum	nan	untreatment	Ovum
CRR556659	T4	embryo	nan	untreatment	1,2,4-cells
CRR556660	T5	embryo	nan	untreatment	64-cells
CRR556661	T6	embryo	nan	untreatment	256-cells
CRR556662	T7	embryo	nan	untreatment	Dome
CRR556663	T8	embryo	nan	untreatment	50% epiboly
CRR556664	T9	embryo	nan	untreatment	75% epiboly
CRR556665	T10	embryo	nan	untreatment	90% epiboly - bud
CRR556666	T11	embryo	nan	untreatment	4-6 somite
CRR556667	T12	embryo	nan	untreatment	15 somite
CRR556668	T13	embryo	nan	untreatment	18-19 somite
CRR556669	T14	embryo	nan	untreatment	25-26 somite
CRR556670	T15	embryo	nan	untreatment	Body rotation
CRR556671	T16	embryo	nan	untreatment	Hatching
CRR556672	T17	larval	nan	untreatment	Eye appearance
CRR556673	T18	larval	nan	untreatment	Larval, 6 days post fertilization
CRR556674	T19	larval	nan	untreatment	Larval, 13 days post fertilization
CRR556675	T20	larval	nan	untreatment	Larval, 20 days post fertilization
CRR556676	HB1	brain	nan	untreatment	Brain, 39 days post fertilization
CRR556680	HM1	muscle	nan	untreatment	Muscle, 39 days post fertilization
CRR556677	HB2	brain	nan	untreatment	Brain, 69 days post fertilization
CRR556684	HL1	liver	nan	untreatment	Liver, 69 days post fertilization
CRR556681	HM2	muscle	nan	untreatment	Muscle, 69 days post fertilization
CRR556678	HB3	brain	nan	untreatment	Brain, 134 days post fertilization
CRR556687	HG1	gill	nan	untreatment	Gill, 134 days post fertilization
CRR556689	HH1	heart	nan	untreatment	Heart, 134 days post fertilization
CRR556691	HI1	intestine	nan	untreatment	Intestine, 134 days post fertilization
CRR556693	HK1	kidney	nan	untreatment	Kidney, 134 days post fertilization
CRR556685	HL2	liver	nan	untreatment	Liver, 134 days post fertilization
CRR556682	HM3	muscle	nan	untreatment	Muscle, 134 days post fertilization
CRR556695	HP1	spleen	nan	untreatment	Spleen, 134 days post fertilization
CRR556697	HS1	skin	nan	untreatment	Skin, 134 days post fertilization
CRR556679	HB4	brain	nan	untreatment	Brain, 197 days post fertilization
CRR556688	HG2	gill	nan	untreatment	Gill, 197 days post fertilization
CRR556690	HH2	heart	nan	untreatment	Heart, 197 days post fertilization
CRR556692	HI2	intestine	nan	untreatment	Intestine, 197 days post fertilization
CRR556694	HK2	kidney	nan	untreatment	Kidney, 197 days post fertilization
CRR556686	HL3	liver	nan	untreatment	Liver, 197 days post fertilization
CRR556683	HM4	muscle	nan	untreatment	Muscle, 197 days post fertilization
CRR556696	HP2	spleen	nan	untreatment	Spleen, 197 days post fertilization
CRR556698	HS2	skin	nan	untreatment	Skin, 197 days post fertilization

challenge

PRJNA234067:

De novo assembly of the grass carp Ctenopharyngodon idella transcriptome to identify miRNA targets associated with motile aeromonad septicemia

key word
- Challenge; RNA-SEQ DATA; IMMUNE-RESPONSE; HEAD KIDNEY; GENES; MICRORNAS; IDENTIFICATION; EXPRESSION; ACTIVATION; INNATE; QUANTIFICATION
publication
- Xu X et al., "De novo assembly of the grass carp Ctenopharyngodon idella transcriptome to identify miRNA targets associated with motile aeromonad septicemia.", PLoS One, 2014;9(11):e112722.
abstract
- Background: De novo transcriptome sequencing is a robust method of predicting miRNA target genes, especially for organisms without reference genomes. Differentially expressed miRNAs had been identified previously in kidney samples collected from susceptible and resistant grass carp (Ctenopharyngodon idella) affected by Aeromonas hydrophila. Target identification for these differentially expressed miRNAs poses a major challenge in this non-model organism. Results: Two cDNA libraries constructed from mRNAs of susceptible and resistant C. idella were sequenced by Illumina Hiseq 2000 technology. A total of more than 100 million reads were generated and de novo assembled into 199,593 transcripts which were further extensively annotated by comparing their sequences to different protein databases. Biochemical pathways were predicted from these transcript sequences. A BLASTx analysis against a non-redundant protein database revealed that 61,373 unigenes coded for 28,311 annotated proteins. Two cDNA libraries from susceptible and resistant samples showed that 721 unigenes were expressed at significantly different levels; 475 were significantly up-regulated and 246 were significantly down-regulated in the SG samples compared to the RG samples. The computational prediction of miRNA targets from these differentially expressed genes identified 188 unigenes as the targets of 5 conserved and 4 putative novel miRNA families. Conclusion: This study demonstrates the feasibility of identifying miRNA targets by transcriptome analysis. The transcriptome assembly data represent a substantial increase in the genomic resources available for C. idella and will provide insights into the gene expression profile analysis and the miRNA function annotations in further studies.

sample list

	sample id	sample name	tissue	strain	treatment	description
	SRR1125014	susceptible (SG) grass carp	spleen and kidney	Aeromonas hydrophila	Aeromonas hydrophila infection	Susceptible grass carp (SG)
	SRR1124206	resistant (RG) grass carp	spleen and kidney	Aeromonas hydrophila	Aeromonas hydrophila infection	Resistant grass carp (RG)

PRJNA246699:

Grass carp ovary cell line (CO) in response to spring viremia of carp virus infection

key word
- Challenge;spring viremia;SVC
publication
- nan
abstract
- nan

sample list

	sample id	sample name	tissue	strain	treatment	description
	SRR1284352	grass carp ovary cell line (CO) in response to spring viremia of carp virus infection	grass carp ovary cell line (CO)	SVCV VR-1390 strain	spring viremia of carp virus infection	Grass carp ovary cell line (CO) in response to spring viremia of carp virus infection
	SRR1286083	grass carp ovary cell line (CO) in response to spring viremia of carp virus infection	grass carp ovary cell line (CO)	SVCV VR-1390 strain	spring viremia of carp virus infection	Grass carp ovary cell line (CO) in response to spring viremia of carp virus infection

PRJNA264233:

The goal is to provide a complete and novel transcriptome dataset of grass carp

key word
- Challenge; GCRV; grass carp reovirus (GCRV); major outer capsid protein VP4; molecular function; host/pathogen protein interaction; RIG-I-like receptor signaling pathway; immune evasion; ENDOPLASMIC-RETICULUM STRESS; GENUS AQUAREOVIRUS; INNATE IMMUNITY; VIRUS; IFN; REVEALS; RECOGNITION; ACTIVATION; PATHWAYS; SEQUENCE
publication
- H Su, et al. "Grass Carp Reovirus Major Outer Capsid Protein VP4 Interacts with RNA Sensor RIG-I to Suppress Interferon Response." Biomolecules10.4(2020).
abstract
- Diseases caused by viruses threaten the production industry and food safety of aquaculture which is a great animal protein source. Grass carp reovirus (GCRV) has caused tremendous loss, and the molecular function of viral proteins during infection needs further research, as for most aquatic viruses. In this study, interaction between GCRV major outer capsid protein VP4 and RIG-I, a critical viral RNA sensor, was screened out by GST pull-down, endogenous immunoprecipitation and subsequent LC-MS/MS, and then verified by co-IP and an advanced far-red fluorescence complementation system. VP4 was proved to bind to the CARD and RD domains of RIG-I and promoted K48-linked ubiquitination of RIG-I to degrade RIG-I. VP4 reducedm RNA and promoter activities of key genes of RLR pathway and sequential IFN production. As a consequence, antiviral effectors were suppressed and GCRV replication increased, resulting in intensified cytopathic effect. Furthermore, results of transcriptome sequencing of VP4 stably expressed CIK (C. idella kidney) cells indicated that VP4 activated the My D88-dependent TLR pathway. Knockdown of VP4 obtained opposite effects. These results collectively revealed that VP4 interacts with RIG-I to restrain interferon response and assist GCRV invasion. This study lays the foundation for anti-dsRNA virus molecular function research in teleost and provides a novel insight into the strategy of immune evasion for aquatic virus.

sample list

sample id	sample name	tissue	strain	treatment	description
SRR1618542	Spleen_susceptible	spleen	Grass carp reovirus (GCRV)	spleen of susceptible fish	Spleen of GCRV-susceptible grass carp
SRR1618520	Spleen_resistant	spleen	Grass carp reovirus (GCRV)	spleen of resistant fish	Spleen of GCRV-resistant grass carp
SRR1618540	Kidney_susceptible	head-kidney	Grass carp reovirus (GCRV)	head-kidney of susceptible fish	Head-kidney of GCRV-susceptible grass carp
SRR1618541	Kidney_resistant	head-kidney	Grass carp reovirus (GCRV)	head-kidney of resistant fish	Head-kidney of GCRV-resistant grass carp

PRJNA288831:

Study aimed at exploring the molecular mechanism of resistance to Aeromonas hydrophila and helping breeding for disease resistance species.

key word
- Challenge; Aeromonas hydrophila; RNA-SEQ ANALYSIS; GRASS CARP; FUNCTIONAL-CHARACTERIZATION; EXPRESSION ANALYSIS; SIGNALING PATHWAY; MOLECULAR-CLONING; TELEOST FISH; IDENTIFICATION; GENES; ANNOTATION
publication
- Dang Y et al., "Transcriptome Analysis of the Innate Immunity-Related Complement System in Spleen Tissue of Ctenopharyngodon idella Infected with Aeromonas hydrophila", Plos One, 2016; 11(7): e0157413.
abstract
- The grass carp (Ctenopharyngodon idella) is an important commercial farmed herbivorous fish species in China, but is susceptible to Aeromonas hydrophila infections. In the present study, we performed de novo RNA-Seq sequencing of spleen tissue from specimens of a disease-resistant family, which were given intra-peritoneal injections containing PBS with or without a dose of A. hydrophila. The fish were sampled from the control group at 0 h, and from the experimental group at 4, 8, 12, 24, 48 and 72 h. 122.18 million clean reads were obtained from the normalized cDNA libraries; these were assembled into 425,260 contigs and then 191,795 transcripts. Of those, 52,668 transcripts were annotated with the NCBI Nr database, and 41,347 of the annotated transcripts were assigned into 90 functional groups. 20,569 unigenes were classified into six main categories, including 38 secondary KEGG pathways. 2,992 unigenes were used in the analysis of differentially expressed genes (DEGs). 89 of the putative DEGs were related to the immune system and 41 of them were involved in the complement and coagulation cascades pathway. This study provides insights into the complement and complement-related pathways involved in innate immunity, through expression profile analysis of the genomic resources in C. idella. We conclude that complement and complement-related genes play important roles during defense against A. hydrophila infection. The immune response is activated at 4 h after the bacterial injections, indicating that the complement pathways are activated at the early stage of bacterial infection. The study has improved our understanding of the immune response mechanisms in C. idella to bacterial pathogens.

sample list

sample id	sample name	tissue	strain	treatment	description
SRR2086445	grass_carp_0	spleen	Aeromonas hydrophila	injected with 1 × PBS	Grass carp infected 0 h (Control)
SRR2086450	grass_carp_12	spleen	Aeromonas hydrophila	100μL intra-peritoneal injections of A. hydrophila	Grass carp infected 12 h
SRR2086456	grass_carp_24	spleen	Aeromonas hydrophila	100μL intra-peritoneal injections of A. hydrophila	Grass carp infected 24 h
SRR2086460	grass_carp_48	spleen	Aeromonas hydrophila	100μL intra-peritoneal injections of A. hydrophila	Grass carp infected 48 h
SRR2086468	grass_carp_4	spleen	Aeromonas hydrophila	100μL intra-peritoneal injections of A. hydrophila	Grass carp infected 4 h
SRR2086471	grass_carp_72	spleen	Aeromonas hydrophila	100μL intra-peritoneal injections of A. hydrophila	Grass carp infected 72 h
SRR2086474	grass_carp_8	spleen	Aeromonas hydrophila	100μL intra-peritoneal injections of A. hydrophila	Grass carp infected 8 h

PRJNA306623:

In order to understand the immunological response of grass carp to infection by A. Hydrophila, the transcriptomic profiles of the spleens from infected and non-infected grass carp groups were obtained.

key word
- Challenge; Ctenopharyngodon idellus; Aeromonas hydrophila; Transcriptome; Pathway analysis; Immune response; TELEOST FISH; COMPLEMENT-SYSTEM; COAGULATION; ACTIVATION; CATHEPSINS; RESPONSES; GENOME; IMMUNE
publication
- Yang Y et al., "Transcriptome profiling of grass carp (Ctenopharyngodon idellus) infected with Aeromonas hydrophila", Fish and Shellfish Immunology, 2016; 51: 329-336.
abstract
- Aeromonas hydrophila is the causative pathogen of intestinal hemorrhage which has caused great economic loss in grass carp aquaculture. In order to understand the immunological response of grass carp to infection by A. hydrophila, the transcriptomic profiles of the spleens from infected and non-infected grass carp groups were obtained using HiSeq™ 2500 (Illumina). An average of 63 million clean reads per library was obtained, and approximately 80% of these genes were successfully mapped to the reference genome. A total of 1591 up-regulated and 530 down-regulated genes were identified. Eight immune-related categories involving 105 differently expressed genes were scrutinized. 16 of the differently expressed genes involving immune response were further validated by qRT-PCR. Our results provide valuable information for further analysis of the mechanisms of grass carp defense against A. hydrophila invasion

sample list

	sample id	sample name	tissue	strain	treatment	description
	SRR3045341	YC_infected	spleen	Aeromonas hydrophila	Aeromonas hydrophila infection.	Grass carp infected by Aeromonas hydrophila.
	SRR3045340	YD_control	spleen	0.65% physiological saline	The fish treated with 0.1ml 0.65% physiological saline.	Grass carp not infected by Aeromonas hydrophila (Control).

PRJNA344676:

In this study, the resistant and susceptible monoclonal CIK cell lines were first established which would be the ponderable research models for the nosogenesis mechanism of the hemorrhagic disease. C1 (CIK cells), R2 (resistant cells) and S3 (susceptible cells) samples were carried out RNA-Seq, MeDIP-Seq and small RNA-Seq by the next-generation sequencing strategy, bioinformatics analysis as well as experimental verification. It was discovered that the aboriginality of CIK cells were gravitated to the susceptible trait. And the discrepancies between resistance and susceptibility against GCRV could primarily attribute to antioxidant activity, cell killing activity and cell proliferation regulation. Here we comprehensively present the profiling and characteristics of DNA methylation and microRNA in the resistant and susceptible CIK cells and proposed that high mCHH methylation distribution might be a characteristic modulator in C. idella. What’s more, a series of genes modulated by DNA methylation or microRNA were designated as potential biomarkers for the resistance breeding. This study laid the foundation and opened novel avenues for nosogenesis research on hemorragic disease of C. idella. Overall design: C1 (CIK cells), R2 (resistant cells) and S3 (susceptible cells) samples were carried out RNA-Seq, MeDIP-Seq and small RNA-Seq by the next-generation sequencing strategy.

key word
- Challenge; GCRV; CIK; GRASS CARP REOVIRUS; MESSENGER-RNA EXPRESSION; ABERRANT DNA METHYLATION; CTENOPHARYNGODON-IDELLA; MICRORNA EXPRESSION; HUMAN-DISEASE; B2 RECEPTOR; GENOME; GENE; RESISTANCE
publication
- Shang X et al., "The destiny of the resistance/susceptibility against GCRV is controlled by epigenetic mechanisms in CIK cells.", Scientific Reports, 2017; 7(1): 4551
abstract
- Hemorrhagic disease caused by grass carp reovirus (GCRV) has severely threatened the grass carp (Ctenopharyngodon idella) cultivation industry. It is noteworthy that the resistance against GCRV infection was reported to be inheritable, and identified at both individual and cellular levels. Therefore, this work was inspired and dedicated to unravel the molecular mechanisms of fate decision post GCRV infection in related immune cells. Foremost, the resistant and susceptible CIK (C. idella kidney) monoclonal cells were established by single cell sorting, subculturing and infection screening successively. RNA-Seq, MeDIP-Seq and small RNA-Seq were carried out with C1 (CIK cells), R2 (resistant cells) and S3 (susceptible cells) groups. It was demonstrated that genome-wide DNA methylation, mRNA and microRNA expression levels in S3 were the highest among three groups. Transcriptome analysis elucidated that pathways associated with antioxidant activity, cell proliferation regulation, apoptosis activity and energy consuming might contribute to the decision of cell fates post infection. And a series of immune-related genes were identified differentially expressed across resistant and susceptible groups, which were negatively modulated by DNA methylation or microRNAs. To conclude, this study systematically uncovered the regulatory mechanism on the resistance from epigenetic perspective and provided potential biomarkers for future studies on resistance breeding.

sample list

sample id	sample name	tissue	strain	treatment	description
SRR4299020	General CIK cells	kidney	control sample	Untreated	General CIK cells (Control)
SRR4299021	Resistant CIK cells	kidney	Grass carp reovirus (GCRV)	GCRV infection	Resistant CIK cells
SRR4299022	Susceptible CIK cells	kidney	Grass carp reovirus (GCRV)	GCRV infection	Susceptible CIK cells

PRJNA359221:

transcriptome sequencing of grass carp that infeceted with two types of GCRV

key word
- Challenge; GCRV; Grass carp; Grass carp reovirus; Transcriptome sequencing; Immune response; Hemorrhage; HEMATOPOIETIC NECROSIS VIRUS; COMPLETE GENOME SEQUENCE; INNATE IMMUNE-RESPONSE; PROKARYOTIC EXPRESSION; COMPLEMENT ACTIVATION; RNA-SEQ; FISH; GENE; INFECTION; PATHWAY
publication
- He L et al., "Differences in responses of grass carp to different types of grass carp reovirus (GCRV) and the mechanism of hemorrhage revealed by transcriptome sequencing" BMC Genomics, 2017; 18: 452.
abstract
- Background: Grass carp is an important farmed fish in China that is affected by serious disease, especially hemorrhagic disease caused by grass carp reovirus (GCRV). The mechanism underlying the hemorrhagic symptoms in infected fish remains to be elucidated. Although GCRV can be divided into three distinct subtypes, differences in the pathogenesis and host immune responses to the different subtypes are still unclear. The aim of this study was to provide a comprehensive insight into the grass carp response to different GCRV subtypes and to elucidate the mechanism underlying the hemorrhagic symptoms. Results: Following infection of grass carp, GCRV-I was associated with a long latent period and low mortality (42.5%), while GCRV-II was associated with a short latent period and high mortality (81.4%). The relative copy number of GCRV-I remained consistent or decreased slightly throughout the first 7 days post-infection, whereas a marked increase in GCRV-II high copy number was detected at 5 days post-infection. Transcriptome sequencing revealed 211 differentially expressed genes (DEGs) in Group I (66 up-regulated, 145 down-regulated) and 670 (386 up-regulated, 284 down-regulated) in Group II. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed significant enrichment in the terms or pathways involved in immune responses and correlating with blood or platelets. Most of the DEGs in Group I were also present in Group II, although the expression profiles differed, with most DEGs showing mild changes in Group I, while marked changes were observed in Group II, especially the interferon-related genes. Many of the genes involved in the complement pathway and coagulation cascades were significantly up-regulated at 7 days post-infection in Group II, suggesting activation of these pathways. Conclusion: GCRV-I is associated with low virulence and a long latent period prior to the induction of a mild host immune response, whereas GCRV-II is associated with high virulence, a short latent period and stimulates a strong and extensive host immune response. The complement and coagulation pathways are significantly activated at 7 days post-infection, leading to the endothelial cell and blood cell damage that result in hemorrhagic symptoms.

sample list

sample id	sample name	tissue	strain	treatment	description
SRR5145951	I-1(1)	spleen	grass carp infected with GCRV-I for one day	infected with GCRV-I	1 day post infected with GCRV-I, replicate 1.
SRR5145952	I-1(2)	spleen	grass carp infected with GCRV-I for one day	infected with GCRV-I	1 day post infected with GCRV-I, replicate 2.
SRR5145953	I-1(3)	spleen	grass carp infected with GCRV-I for one day	infected with GCRV-I	1 day post infected with GCRV-I, replicate 3.
SRR5145954	I-3(1)	spleen	grass carp infected with GCRV-I for three days	infected with GCRV-I	3 days post infected with GCRV-I, replicate 1.
SRR5145955	I-3(2)	spleen	grass carp infected with GCRV-I for three days	infected with GCRV-I	3 days post infected with GCRV-I, replicate 2.
SRR5145957	I-3(3)	spleen	grass carp infected with GCRV-I for three days	infected with GCRV-I	3 days post infected with GCRV-I, replicate 3.
SRR5145958	I-5(1)	spleen	grass carp infected with GCRV-I for five days	infected with GCRV-I	5 days post infected with GCRV-I, replicate 1.
SRR5145959	I-5(2)	spleen	grass carp infected with GCRV-I for five days	infected with GCRV-I	5 days post infected with GCRV-I, replicate 2.
SRR5145960	I-5(3)	spleen	grass carp infected with GCRV-I for five days	infected with GCRV-I	5 days post infected with GCRV-I, replicate 3.
SRR5145961	I-7(1)	spleen	grass carp infected with GCRV-I for seven days	infected with GCRV-I	7 days post infected with GCRV-I, replicate 1.
SRR5145962	I-7(2)	spleen	grass carp infected with GCRV-I for seven days	infected with GCRV-I	7 days post infected with GCRV-I, replicate 2.
SRR5145963	I-7(3)	spleen	grass carp infected with GCRV-I for seven days	infected with GCRV-I	7 days post infected with GCRV-I, replicate 3.
SRR5145996	II-1(1)	spleen	grass carp infected with GCRV-II for one day	infected with GCRV-II	1 day post infected with GCRV-II, replicate 1.
SRR5145997	II-1(2)	spleen	grass carp infected with GCRV-II for one day	infected with GCRV-II	1 day post infected with GCRV-II, replicate 2.
SRR5145998	II-1(3)	spleen	grass carp infected with GCRV-II for one day	infected with GCRV-II	1 day post infected with GCRV-II, replicate 3.
SRR5145999	II-3(1)	spleen	grass carp infected with GCRV-II for three days	infected with GCRV-II	3 days post infected with GCRV-II, replicate 1.
SRR5146000	II-3(2)	spleen	grass carp infected with GCRV-II for three days	infected with GCRV-II	3 days post infected with GCRV-II, replicate 2.
SRR5146001	II-3(3)	spleen	grass carp infected with GCRV-II for three days	infected with GCRV-II	3 days post infected with GCRV-II, replicate 3.
SRR5146003	II-5(1)	spleen	grass carp infected with GCRV-II for five days	infected with GCRV-II	5 days post infected with GCRV-II, replicate 1.
SRR5146004	II-5(2)	spleen	grass carp infected with GCRV-II for five days	infected with GCRV-II	5 days post infected with GCRV-II, replicate 2.
SRR5146005	II-5(3)	spleen	grass carp infected with GCRV-II for five days	infected with GCRV-II	5 days post infected with GCRV-II, replicate 3.
SRR5146006	II-7(1)	spleen	grass carp infected with GCRV-II for seven days	infected with GCRV-II	7 days post infected with GCRV-II, replicate 1.
SRR5146007	II-7(2)	spleen	grass carp infected with GCRV-II for seven days	infected with GCRV-II	7 days post infected with GCRV-II, replicate 2.
SRR5146008	II-7(3)	spleen	grass carp infected with GCRV-II for seven days	infected with GCRV-II	7 days post infected with GCRV-II, replicate 3.
SRR5146010	C-1(1)	spleen	control sample for one day	control	1 day post injected with PBS, replicate 1 (Control).
SRR5146011	C-1(2)	spleen	control sample for one day	control	1 day post injected with PBS, replicate 2 (Control).
SRR5146012	C-1(3)	spleen	control sample for one day	control	1 day post injected with PBS, replicate 3 (Control).
SRR5146013	C-3(1)	spleen	control sample for three days	control	3 days post injected with PBS, replicate 1 (Control).
SRR5146014	C-3(2)	spleen	control sample for three days	control	3 days post injected with PBS, replicate 2 (Control).
SRR5146015	C-3(3)	spleen	control sample for three days	control	3 days post injected with PBS, replicate 3 (Control).
SRR5146017	C-5(1)	spleen	control sample for five days	control	5 days post injected with PBS, replicate 1 (Control).
SRR5146018	C-5(2)	spleen	control sample for five days	control	5 days post injected with PBS, replicate 2 (Control).
SRR5146019	C-5(3)	spleen	control sample for five days	control	5 days post injected with PBS, replicate 3 (Control).
SRR5146020	C-7(1)	spleen	control sample for seven days	control	7 days post injected with PBS, replicate 1 (Control).
SRR5146031	C-7(2)	spleen	control sample for seven days	control	7 days post injected with PBS, replicate 2 (Control).
SRR5146032	C-7(3)	spleen	control sample for seven days	control	7 days post injected with PBS, replicate 3 (Control).

PRJNA392988:

Transcriptome sequencing of CIK cells infected with GCRV

key word
- Challenge; CIK; GCRV; grass carp; grass carp reovirus; transcriptomics sequencing; phagosome; FOCAL ADHESION KINASE; CTENOPHARYNGODON-IDELLUS; SUBUNIT VACCINE; VIRUS-INFECTION; AUTOIMMUNITY; RECEPTORS; IMMUNITY; ROLES
publication
- Chen G et al., "Transcriptomics Sequencing Provides Insights into Understanding the Mechanism of Grass Carp Reovirus Infection", International Journal of Molecular Sciences, 2018; 19(2): 488.
abstract
- Grass carp is an important aquaculture fish species in China that is affected by severe diseases, especially haemorrhagic disease caused by grass carp reovirus (GCRV). However, the mechanisms of GCRV invasion and infection remain to be elucidated. In the present study, Ctenopharyngodon idellus kidney (CIK) cells were infected with GCRV, harvested at 0, 8, 24, and 72 h post infection, respectively, and then subjected to transcriptomics sequencing. Each sample yielded more than 6 Gb of clean data and 40 million clean reads. To better understand GCRV infection, the process was divided into three phases: the early (0–8 h post infection), middle (8–24 h post infection), and late (24–72 h) stages of infection. A total of 76 (35 up-regulated, 41 down-regulated), 553 (463 up-regulated, 90 down-regulated), and 284 (150 up-regulated, 134 down-regulated) differently expressed genes (DEGs) were identified during the early, middle, and late stages of infection, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that DEGs were mainly involved in carbohydrate biosynthesis, transport, and endocytosis in the early stage, phagocytosis and lysosome pathways were mainly enriched in the middle stage, and programmed cell death, apoptosis, and inflammation were largely associated with the late stage. These results suggest GCRV infection is a gradual process involving adsorption on the cell surface, followed by endocytosis into cells, transport by lysosomes, and eventually resulted in cell necrosis and/or apoptosis. Our findings provide insight into the mechanisms of grass carp reovirus infection.

sample list

sample id	sample name	tissue	strain	treatment	description
SRR5803047	C0	kidney cells	Grass carp reovirus (GCRV)	GCRV infection for 0h	CIK cells infected with GCRV (not trusted)
SRR5803830	C0	kidney cells	Grass carp reovirus (GCRV)	GCRV infection for 4h	CIK cells infected with GCRV (not trusted)
SRR5803832	C0	kidney cells	Grass carp reovirus (GCRV)	GCRV infection for 8h	CIK cells infected with GCRV (not trusted)
SRR5803833	C0	kidney cells	Grass carp reovirus (GCRV)	GCRV infection for 24h	CIK cells infected with GCRV (not trusted)
SRR5803834	C0	kidney cells	Grass carp reovirus (GCRV)	GCRV infection for 3d	CIK cells infected with GCRV (not trusted)

PRJNA476389:

To understand the effects of Grass carp reovirus （GCRV） infection on transcriptions of grass carp genes, RNA-seq of CIK cells infected with Grass carp reovirus JX01 or overexpressed with viral encoding protein NS31 was carried out.

key word
- Challenge; GCRV; CIK; Aquareovirus; NS31; Heat-shock response; HSP70; CELLULAR HEAT-SHOCK-PROTEIN-70; VIRUS; HSP70; ACTIVATION; POLYMERASE; CHAPERONES; ADENOVIRUS; PROMOTERS; MECHANISM
publication
- Yu F etal., "Aquareovirus NS31 protein serves as a specific inducer for host heat shock 70-kDa protein", Journal of General Virology, 2020; 101:145-155
abstract
- Elevation of heat-shock protein expression, known as cellular heat-shock responses, occurs during infection of many viruses. which is involved in viral replication through various mechanisms. Herein, transcriptome analysis revealed that over-expression of non-structural protein NS31 of grass carp reovirus (GCRV) in grass carp Ctenopharyngodon idellus kidney (CIK) cells specifically induced expression of heat-shock response (HSR) genes HSP30 and HSP70. We further found that, among the HSR genes, only HSP70 protein were shown to be efficiently induced in fish cells following NS31 over-expression or GCRV infection. Employing a luciferase assay, we were able to show that the promoter of the HSP70 gene can be specifically activated by NS31. In addition, over-expressing HSP70 in grass carp CIK cells resulted in enhanced replication efficiency of GCRV, and an inhibitor for HSP70 resulted in the inhibition of GCRV replication, indicating that HSP70 should serve as a pro-viral factor. We also found that NS31 could activate HSP70 expression in cells of other vertebrate animals. Similar inducing effect on HSP70 expression was demonstrated for NS31-homologue proteins of other aquareoviruses including American grass carp reovirus (AGCRV) and GRCV (green river chinook virus). All these results indicated NS31 proteins in the Aquareovirus genus should play a key role for up-regulating specific HSP70 gene during viral replication.

sample list

sample id	sample name	tissue	strain	treatment	description
SRR7349858	GCRV20h	kidney cells	Grass carp reovirus (GCRV)	GCRV for 20h	GCRV for 20h
SRR7349859	GFP	kidney cells	Grass carp reovirus (GCRV)	pEGFP-N1 and G418	pEGFP-N1 and G418
SRR7349860	NS31GFP	kidney cells	Grass carp reovirus (GCRV)	pEGFP-N1-NS31 and G418	pEGFP-N1-NS31 and G418
SRR7349861	GCRVmock	kidney cells	Grass carp reovirus (GCRV)	Mock infection	Mock infection
SRR7349862	GCRV12h	kidney cells	Grass carp reovirus (GCRV)	GCRV for 12h	GCRV for 12h

PRJNA513222:

Bacillus subtilis is a usual group of probiotics that have been widely used in the feed industry, it can increase host resistance to pathogens and balance the immune responses. But the regulatory mechanism of Bacillus subtilis on the host immune system remains unclear in teleost. In this data, we collected Bacillus subtilis stimulated grass carp DCs at 0, 4, and 18 h, constructed and sequenced transcriptomic libraries respectively. This study provides a DCs-specific transcriptome data in grass carp by Bacillus subtilis stimulation, allowing us to illustrate the molecular mechanism of DCs-mediated immune response triggered by probiotics in grass carp.

key word
- Challenge; dendritic cell; Ctenopharyngodon idella; Bacillus subtilis; cytokine; transcriptome; PROBIOTIC BACTERIA; T-CELLS; ULCERATIVE-COLITIS; IN-VITRO; RESPONSES; RECEPTOR; IDENTIFICATION; PEPTIDOGLYCAN; MACROPHAGES; POPULATION
publication
- Zhou C et al., "Regulatory Effect of Bacillus subtilis on Cytokines of Dendritic Cells in Grass Carp (Ctenopharyngodon Idella)", International Journal of Molecular Sciences, 2019; 20: 389.
abstract
- Bacillus subtilis is a common group of probiotics that have been widely used in the feed industry as they can increase host resistance to pathogens and balance the immune response. However, the regulatory mechanism of Bacillus subtilis on the host immune system remains unclear in teleosts. In this study, we isolated and enriched dendritic cells from white blood cells (WBCs), and then stimulated them with Bacillus subtilis. Morphological features, specific biological functions, and authorized functional molecular markers were used in the identification of dendritic cells. Subsequently, we collected stimulated cells at 0, 4, and 18 h, and then constructed and sequenced the transcriptomic libraries. A transcriptome analysis showed that 2557 genes were up-regulated and 1708 were down-regulated at 4 h compared with the control group (|Fold Change| ≥ 4), and 1131 genes were up-regulated and 1769 were down-regulated between the cells collected at 18 h and 4 h (|Fold Change| ≥ 4). Gene Ontology (GO) annotations suggested many differentially expressed genes (DEGs) (p < 0.05 and |Fold Change| ≥ 4) were involved in immune-related biological functions including immune system progress, cytokine receptor binding, and cytokine binding. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the cytokine⁻cytokine receptor interaction pathways were significantly enriched at both time points (p < 0.05), which may play a key role in the response to stimulation. Furthermore, mRNA expression level examination of several pro-inflammatory cytokines and anti-inflammatory cytokines genes by quantitative real-time polymerase chain reaction (qRT-PCR) indicated that their expressions can be significantly increased in Bacillus subtili, which suggest that Bacillus subtilis can balance immune response and tolerance. This study provides dendritic cell (DC)-specific transcriptome data in grass carp by Bacillus subtilis stimulation, allowing us to illustrate the molecular mechanism of the DC-mediated immune response triggered by probiotics in grass carp.

sample list

sample id	sample name	tissue	strain	treatment	description
SRR8402455	EG4h2	spleen	Bacillus subtilis	DCs exposed to Bacillus subtilis for 4 hours	DCs exposed to Bacillus subtilis for 4 hours, replicate 2
SRR8402456	EG4h3	spleen	Bacillus subtilis	DCs exposed to Bacillus subtilis for 4 hours	DCs exposed to Bacillus subtilis for 4 hours, replicate 3
SRR8402457	EG18h1	spleen	Bacillus subtilis	DCs exposed to Bacillus subtilis for 18 hours	DCs exposed to Bacillus subtilis for 18 hours, replicate 1
SRR8402458	EG18h2	spleen	Bacillus subtilis	DCs exposed to Bacillus subtilis for 18 hours	DCs exposed to Bacillus subtilis for 18 hours, replicate 2
SRR8402459	Con1	spleen	Bacillus subtilis	untreatment	Control, replicate 1
SRR8402460	Con2	spleen	Bacillus subtilis	untreatment	Control, replicate 2
SRR8402461	Con3	spleen	Bacillus subtilis	untreatment	Control, replicate 3
SRR8402462	EG4h1	spleen	Bacillus subtilis	DCs exposed to Bacillus subtilis for 4 hours	DCs exposed to Bacillus subtilis for 4 hours, replicate 1
SRR8402463	EG18h3	spleen	Bacillus subtilis	DCs exposed to Bacillus subtilis for 18 hours	DCs exposed to Bacillus subtilis for 18 hours, replicate 3

PRJNA580128:

Gut microbiota modulation and immunity response induced by Citrobacter freundii in grass carp

key word
- Challenge; Gut microbiota; Citrobacter freundii; Immune response; Goblet cells; Grass carp; COMPLEMENT; INFECTION; STRINGTIE; SYSTEM; HEALTH; HISAT
publication
- Xiong F et al., "Gut microbiota modulation and immunity response induced by Citrobacter freundii strain GC01 in grass carp (Ctenopharyngodon idellus)", Aquaculture, 2020; 521(15):735010.
abstract
- The effect of Citrobacter freundii, an opportunistic pathogen of fish, on the gut microbiota and immune responses in fish remains unknown. We fed grass carp (Ctenopharyngodon idellus) with two different concentrations of this bacterium (experimental Low and High groups, plus Control group). No signs of acute inflammatory response were found in either of the experimental groups using the intestinal HE staining method, but the number of intestinal goblet cells was much higher in the High group. Furthermore, we found that feeding C. freundii significantly decreased the alpha diversity and altered beta diversity of gut microbiota in both groups, and significantly promoted the relative abundance of Enterobacteriales, Pasteurellales, Neisseriales and Citrobacter in the High group. Spleen transcriptome showed that the expression pattern of immune system-related genes varied significantly between the Control group and High group. Several immunity-related pathways and two infectious diseases-related pathways were significantly enriched in the High group. Many complement system genes, including c3, c4, c5, c7, c8a, c8b and c1s, were also up-regulated in the High group. Overall, our results indicate that C. freundii did not trigger acute intestinal inflammation, but it changed the diversity and population structure of gut microbiota, and triggered the host's innate mucosal immune system. The enrichment of two infectious diseases-related pathways also suggested a higher risk of infection in the High group. These results contribute to our understanding of the effects of opportunistic fish pathogens on gut microbiota and host's immune responses.

sample list

sample id	sample name	tissue	strain	treatment	description
SRR11613380	High3	spleen	Citrobacter freundii	Fed with high concentration Citrobacter freundii	Fed with high concentration Citrobacter freundii, replicate 3
SRR11613381	High2	spleen	Citrobacter freundii	Fed with high concentration Citrobacter freundii	Fed with high concentration Citrobacter freundii, replicate 2
SRR11613382	High1	spleen	Citrobacter freundii	Fed with high concentration Citrobacter freundii	Fed with high concentration Citrobacter freundii, replicate 1
SRR11613383	Con2	spleen	Citrobacter freundii	untreatment	Control, replicate 2
SRR11613384	Con1	spleen	Citrobacter freundii	untreatment	Control, replicate 1
SRR11613385	Low5	spleen	Citrobacter freundii	Fed with low concentration Citrobacter freundii	Fed with low concentration Citrobacter freundii, replicate 5
SRR11613386	Low4	spleen	Citrobacter freundii	Fed with low concentration Citrobacter freundii	Fed with low concentration Citrobacter freundii, replicate 4
SRR11613387	Low3	spleen	Citrobacter freundii	Fed with low concentration Citrobacter freundii	Fed with low concentration Citrobacter freundii, replicate 3
SRR11613388	Low2	spleen	Citrobacter freundii	Fed with low concentration Citrobacter freundii	Fed with low concentration Citrobacter freundii, replicate 2
SRR11613389	Low1	spleen	Citrobacter freundii	Fed with low concentration Citrobacter freundii	Fed with low concentration Citrobacter freundii, replicate 1
SRR11613390	Con5	spleen	Citrobacter freundii	untreatment	Control, replicate 5
SRR11613391	Con4	spleen	Citrobacter freundii	untreatment	Control, replicate 4
SRR11613392	Con3	spleen	Citrobacter freundii	untreatment	Control, replicate 3
SRR11613393	High5	spleen	Citrobacter freundii	Fed with high concentration Citrobacter freundii	Fed with high concentration Citrobacter freundii, replicate 5
SRR11613394	High4	spleen	Citrobacter freundii	Fed with high concentration Citrobacter freundii	Fed with high concentration Citrobacter freundii, replicate 4

PRJNA597579: