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Sample GSM5260394 Query DataSets for GSM5260394
Status Public on Apr 01, 2023
Title 2y3_muscle
Sample type SRA
 
Source name breast muscle
Organism Columba livia
Characteristics strain: White-King pigeon
tissue: breast muscle
age: 2 years 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 SAMN18835497
SRA SRX10659597

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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