|
| Status |
Public on Sep 12, 2021 |
| Title |
1D-3_bursa of Fabricius |
| Sample type |
SRA |
| |
|
| Source name |
bursa of Fabricius
|
| Organism |
Columba livia |
| Characteristics |
strain: White-King pigeon
tissue: bursa of Fabricius
developmental stage: 1 day old
|
| Treatment protocol |
The samples for subsequent transcriptome sequencing were frozen in liquid nitrogen and stored at -80℃ refrigerator.
|
| Growth protocol |
The pigeons were grouped into three developmental stages: 1 day (1D), 13 days (13D) and 26 days (26D).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was respectively isolated from frozen BF samples collected from 9 female pigeon squabs across the three developmental stages (3 biological replicates each) by HiPure Universal RNA Kit (Magen, Guangzhou, China) according to the manufacturer's protocol.
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 to the pigeon genome (Cliv_1.0 from NCBI) using STAR (v.2.6.0c)
Mapped reads were assembled to transcripts using the Cufflinks (v.2.1.1) software . The transcripts ( ≤250 bp or FPKM < 0.1) were first excluded.The remaining transcripts were merged and compared to the reference genome by the meta-assembly tool TACO software (v0.7.3)
Those transcripts un-annotated by protein-coding genes (PCGs) were retained as putatively lncRNA transcripts.Subsequently, Coding Potential Calculator (CPC2) and PfamScan were applied to predict the coding potential of these transcripts.
After removing transcripts with coding capacities, the remaining transcripts were identified to be long non-coding RNAs.
Genome_build: Cliv_1.0
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample
|
| |
|
| Submission date |
Sep 09, 2021 |
| Last update date |
Sep 12, 2021 |
| Contact name |
Xun Wang |
| E-mail(s) |
xunwang@sicau.edu.cn
|
| Phone |
+862882707606
|
| Organization name |
Sichuan agricultural university
|
| Street address |
Huimin road 211#, Wenjiang district
|
| City |
Chengdu |
| State/province |
China |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
|
| Platform ID |
GPL29485 |
| Series (1) |
| GSE183791 |
Transcriptome analysis reveals the roles of long non-coding RNA and mRNA in bursa of Fabricius during pigeon (Columba livia) development |
|
| Relations |
| BioSample |
SAMN21368493 |
| SRA |
SRX12122689 |
