|
| Status |
Public on Jul 27, 2021 |
| Title |
19_Resting_aDP_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Adult contour feather (apical dermal papilla from Resting phase)
|
| Organism |
Gallus gallus |
| Characteristics |
breed: white leghorn
tissue: Apical dermal papilla from Resting phase
Sex: male
group: 2
|
| 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 |
Apical dermal papilla from Resting phase rep1
|
| 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 |
SAMN16729275 |
| SRA |
SRX9471113 |
