|
| Status |
Public on Apr 27, 2021 |
| Title |
Granulosa_ZT0_3 |
| Sample type |
SRA |
| |
|
| Source name |
Granulosa cells
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: Chicken follicle
cell type: Granulosa cells
time: 9:00 AM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Granulosa cells were collected and put into liquid nitrogen immediately from preovulatory follicles (F1). For total RNA sequencing, about 4 μg total RNA was isolated from the granulosa cells (a total of 9 samples) by using TRIzol reagent (Invitrogen, USA) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Clean reads were mapped against chicken reference genome using STAR v2.6.0c and merged with Cuffmerge (Cufflinks v2.2.1).
Assemblyline and TACO to filter transcripts and merge all expressed transcripts
Remove transcripts of coding gene while comparing to annotated genome by Cuffcompare
The prediction and calculation of the coding potential of the remaining transcripts by CPC2
Comparing with the Pfam-31A database and trimming out transcripts with a p-value < 10-4 by Hmmscan
Genome_build: STAR v2.6.0c
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample
|
| |
|
| Submission date |
Jun 11, 2020 |
| Last update date |
Apr 27, 2021 |
| Contact name |
Liang Li |
| Organization name |
Sichuan agricultural university
|
| Street address |
Wenjiangqu huiminlu211hao sichuan nongyedaxue
|
| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
|
| Platform ID |
GPL26853 |
| Series (1) |
| GSE152268 |
Systematic Analysis of Long Noncoding RNA and mRNA in Granulosa Cells During the Hen Ovulatory Cycle |
|
| Relations |
| BioSample |
SAMN15214137 |
| SRA |
SRX8530424 |
