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Sample GSM3021720 Query DataSets for GSM3021720
Status Public on Feb 25, 2018
Title Rhesus Macaque 4 - CD4+ T-cells Untreated
Sample type SRA
Source name Primary Pan-CD4+ cells isolated by positive selection of the CD4 antigen
Organism Macaca mulatta
Characteristics tissue: CD4+ T-cells
species: R. Macaque
individual: 4
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 NextSeq 500
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 (*
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 Feb 25, 2018
Last update date Feb 26, 2018
Contact name Charles G Danko
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 GPL21120
Series (1)
GSE85337 Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells
BioSample SAMN08605589
SRA SRX3740874

Supplementary file Size Download File type/resource 53.9 Mb (ftp)(http) BW 55.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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