|
| Status |
Public on Dec 29, 2016 |
| Title |
Chimp 3 - CD4+ T-cells Untreated |
| Sample type |
SRA |
| |
|
| Source name |
Primary Pan-CD4+ cells isolated by positive selection of the CD4 antigen
|
| Organism |
Pan troglodytes |
| Characteristics |
tissue: CD4+ T-cells
species: Chimp
individual: 3
treatment: Untreated
|
| Treatment protocol |
Cells were treated for 30 minutes with ethanol+DMSO or PMA+Ionomycin.
|
| Growth protocol |
CD4+ T-cells isolated from peripheral blood using positive selection for the CD4 antigen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclei were isolated using the protocol in Danko et. al. (2013) Nature Methods.
We prepared PRO-seq libraries as described in Kwak et. al. (2013) Science.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
library strategy: PRO-seq
nascent RNA
|
| Data processing |
We trimmed adapter sequences and mapped PRO-seq data using BWA.
Data was converted into bigWig format and converted to reads per kilobase per million mapped (RPKM).
dREG (v. 1.0) was used to identify TREs using the indicated dataset (*TSS.bw).
Genome_build: hg19
Genome_build: panTro4
Genome_build: rheMac3
Genome_build: mm10
Genome_build: rn6
Supplementary_files_format_and_content: Raw dREG scores, peak calls, and PRO-seq or GRO-seq data are provided in standard bigWig or BED file formats.
|
| |
|
| Submission date |
Aug 08, 2016 |
| Last update date |
Feb 25, 2018 |
| Contact name |
Charles G Danko |
| E-mail(s) |
dankoc@gmail.com
|
| Organization name |
Cornell University
|
| Department |
Baker Institute
|
| Lab |
Danko Lab
|
| Street address |
Hungerford Hill Rd
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL16809 |
| Series (1) |
| GSE85337 |
Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells |
|
| Relations |
| BioSample |
SAMN05525793 |
| SRA |
SRX2008414 |
