Bioproject ID: PRJCA010000

bioproject id PRJCA010000      to NCBI
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
experiment type baseline
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)
description Grass carp development
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 Information

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