|
Status |
Public on Jul 27, 2021 |
Title |
12_cPP_rep3 |
Sample type |
SRA |
|
|
Source name |
Adult contour feather (central pulp)
|
Organism |
Gallus gallus |
Characteristics |
breed: white leghorn tissue: Central pulp Sex: male group: 1
|
Treatment protocol |
No treatment
|
Growth protocol |
1 year old adult male white leghorn chicken
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA extraction for RNA-seq: Total RNAs of indicated tissues were extracted followed by the standard Trizol extraction protocol (Invitrogen, Cat.15596026). TruSeq RNA Prep Kit v2 (Illumina, RS-122-2001/-2002).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
Central pulp rep3
|
Data processing |
RNA-seq analysis. The RNA-seq analysis pipeline was adapted according to the publication (Trapnell et al., 2012). Manipulation. Tools: fastq_groomer (Galaxy Version 1.1.1) and fastq_trimmer_by_quality (window size 3; min score >= 20). Mapping. Tool: TopHat2 (Galaxy Version 2.1.1). Quantification and differentially expressed gene analysis. Tools: Cufflinks package (Trapnell et al., 2010)–including Cufflinks (Galaxy Version 2.2.1.2), Cuffmerge (Galaxy Version 2.2.1.1), Cuffquant (Galaxy Version 2.2.1.1), and Cuffdiff (Galaxy Version 2.2.1.3). Supplementary_files_format_and_content: TPM
|
|
|
Submission date |
Nov 10, 2020 |
Last update date |
Jul 27, 2021 |
Contact name |
Ping Wu |
E-mail(s) |
pingwu@usc.edu
|
Phone |
6264979629
|
Organization name |
University of Southern California
|
Department |
Pathology
|
Street address |
2011 Zonal Ave HMR313A
|
City |
Los Angeles |
State/province |
CA |
ZIP/Postal code |
90033 |
Country |
USA |
|
|
Platform ID |
GPL19787 |
Series (1) |
GSE161220 |
Regeneration of dermal papilla stem cells and mesenchymal components during feather cycling |
|
Relations |
BioSample |
SAMN16729282 |
SRA |
SRX9471106 |