Bioproject ID: PRJNA435500

bioproject id PRJNA435500      to NCBI
key word Baseline; rainbow trout; red blood cells; RNA-seq; de novo assembly; transcriptome; peptide fractionation; LC ESI-MSMS; proteome; functional network; immune response; CD-HIT; ERYTHROCYTES; PROTEIN; ANNOTATION; EXPRESSION; CYTOSCAPE
experiment type baseline
publication Sara, P. M. , et al. "In Silico Functional Networks Identified in Fish Nucleated Red Blood Cells by Means of Transcriptomic and Proteomic Profiling." Genes 9.4(2018):1.
description Transcriptome assembly data for Oncorhynchus mykiss red blood cells
abstract Nucleated red blood cells (RBCs) of fish have, in the last decade, been implicated in several immune-related functions, such as antiviral response, phagocytosis or cytokine-mediated signaling. RNA-sequencing (RNA-seq) and label-free shotgun proteomic analyses were carried out for in silico functional pathway profiling of rainbow trout RBCs. For RNA-seq, a de novo assembly was conducted, in order to create a transcriptome database for RBCs. For proteome profiling, we developed a proteomic method that combined: (a) fractionation into cytosolic and membrane fractions, (b) hemoglobin removal of the cytosolic fraction, (c) protein digestion, and (d) a novel step with pH reversed-phase peptide fractionation and final Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometric (LC ESI-MS/MS) analysis of each fraction. Combined transcriptome- and proteome- sequencing data identified, in silico, novel and striking immune functional networks for rainbow trout nucleated RBCs, which are mainly linked to innate and adaptive immunity. Functional pathways related to regulation of hematopoietic cell differentiation, antigen presentation via major histocompatibility complex class II (MHCII), leukocyte differentiation and regulation of leukocyte activation were identified. These preliminary findings further implicate nucleated RBCs in immune function, such as antigen presentation and leukocyte activation.

Sample Information

sample id sample name tissue strain treatment description
1. SRR9644930 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
2. SRR9645023 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
3. SRR9645024 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
4. SRR9645025 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
5. SRR9645026 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
6. SRR9645027 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
7. SRR9645028 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
8. SRR9645029 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
9. SRR9645030 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
10. SRR9644929 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
11. SRR9644931 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
12. SRR9644932 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
13. SRR9644934 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
14. SRR9644935 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
15. SRR9644936 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
16. SRR6806638 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
17. SRR6806639 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
18. SRR6806642 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
19. SRR8164499 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
20. SRR8164502 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
21. SRR8164496 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
22. SRR8164498 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
23. SRR6806637 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
24. SRR6806641 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
25. SRR8164503 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
26. SRR9644933 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
27. SRR8164501 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
28. SRR7262889 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
29. SRR7262891 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
30. SRR7262892 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
31. SRR7262893 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
32. SRR7262894 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
33. SRR6806640 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
34. SRR8164500 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
35. SRR7262890 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
36. SRR8164497 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
37. SRR6806636 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan