|
| Status |
Public on Apr 01, 2023 |
| Title |
14d2_muscle |
| Sample type |
SRA |
| |
|
| Source name |
breast muscle
|
| Organism |
Columba livia |
| Characteristics |
strain: White-King pigeon
tissue: breast muscle
age: 14 days old
|
| Treatment protocol |
The breast muscle of pigeon was collected and then frozen in liquid nitrogen rapidly.
|
| Growth protocol |
The pigeons were grouped into four developmental stages: 1 day (1D), 14 days (14D), 28 days (28D), and 2 years old (2Y).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen breast muscle samples using Trizol reagent according to 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 HiSeq 4000 |
| |
|
| Description |
quant_lnc.tpm_0.1.txt
quant_mRNA.tpm_0.5.txt
|
| Data processing |
Clean data were aligned to the pigeon (Columba livia) genome (Cliv_1.0) using STAR. Transcripts were ab initio assembled using the Cufflinks software. For long non-coding RNA identification, transcripts that were clipped (first or last exons <15 bp), with short lengths or in a lowly abundance were discarded as poorly assembled ones for each sample. Secondly, transcripts were merged and compared to the reference genome by TACO software and those transcripts un-annotated by protein-coding genes (PCGs) were kept as putatively lncRNA transcripts. Thirdly, CPC2 was used to perform coding potential analysis, and PfamScan was applied to check the domain hits of the nucleic acid sequences against the Pfam database after open reading frames were obtained utilizing EMBOSS. A domain hit by PCGs and putative lncRNAs were checked by Fisher's exact test, and those domains with an odds ratio of less than 10.0 or P value greater than 0.05 were considered as likely artifacts. After removing transcripts in all likely domains and with coding potential, the remains were identified to be lncRNAs.
|
| |
|
| Submission date |
Apr 22, 2021 |
| Last update date |
Apr 01, 2023 |
| Contact name |
Yi Luo |
| E-mail(s) |
306361896@qq.com
|
| Organization name |
Sichuan Agricultural University
|
| Street address |
gongpin road #211
|
| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
|
| Platform ID |
GPL30596 |
| Series (1) |
| GSE173122 |
Identification and expression pattern of mRNAs and lncRNAs in breast muscle during pigeon (Columba livia) development. |
|
| Relations |
| BioSample |
SAMN18835491 |
| SRA |
SRX10659590 |
