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Series GSE85337 Query DataSets for GSE85337
Status Public on Dec 29, 2016
Title Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells
Organisms Macaca mulatta; Pan troglodytes; Homo sapiens; Mus musculus; Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Summary Transcriptional regulatory changes have been shown to contribute to phenotypic differences between species, but many questions remain about how gene expression evolves. Here we report the first comparative study of nascent transcription in primates. We used PRO-seq to map actively transcribing RNA polymerases in resting and activated CD4+ T-cells in multiple human, chimpanzee, and rhesus macaque individuals, with rodents as outgroups. This approach allowed us to directly measure active transcription separately from post-transcriptional processes. We observed general conservation in coding and non-coding transcription, punctuated by numerous differences between species, particularly at distal enhancers and non-coding RNAs. Transcription factor binding sites are a primary determinant of transcriptional differences between species. We found evidence for stabilizing selection on gene expression levels and adaptive substitutions associated with lineage-specific transcription. Finally, rates of evolutionary change are strongly correlated with long-range chromatin interactions. These observations clarify the role of primary transcription in regulatory evolution.
Overall design We analyzed collected PRO-seq data from CD4+ T-cells isolated from five mammalian species in two conditions.
Contributor(s) Danko CG
Citation(s) 29379187, 28049628
Submission date Aug 08, 2016
Last update date Jul 12, 2019
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
Platforms (8)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL14954 Illumina HiSeq 2000 (Macaca mulatta)
GPL16809 Illumina HiSeq 2000 (Pan troglodytes)
Samples (24)
GSM2265095 Human 1 - CD4+ T-cells Untreated
GSM2265096 Human 1 - CD4+ T-cells PMA+Ionomycin
GSM2265097 Human 2, draw 1 - CD4+ T-cells PMA+Ionomycin
BioProject PRJNA338193
SRA SRP081110

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MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource 84.6 Mb (ftp)(http) BW 82.5 Mb (ftp)(http) BW 132.6 Mb (ftp)(http) BW 136.2 Mb (ftp)(http) BW 135.5 Mb (ftp)(http) BW 140.0 Mb (ftp)(http) BW 96.8 Mb (ftp)(http) BW 94.4 Mb (ftp)(http) BW 153.1 Mb (ftp)(http) BW 157.0 Mb (ftp)(http) BW 156.6 Mb (ftp)(http) BW 161.3 Mb (ftp)(http) BW 77.3 Mb (ftp)(http) BW 120.9 Mb (ftp)(http) BW 125.0 Mb (ftp)(http) BW 82.8 Mb (ftp)(http) BW 130.9 Mb (ftp)(http) BW 134.1 Mb (ftp)(http) BW 20.4 Mb (ftp)(http) BW 21.0 Mb (ftp)(http) BW 74.1 Mb (ftp)(http) BW 67.4 Mb (ftp)(http) BW 99.0 Mb (ftp)(http) BW 94.8 Mb (ftp)(http) BW 99.0 Mb (ftp)(http) BW 98.0 Mb (ftp)(http) BW 96.0 Mb (ftp)(http) BW 86.8 Mb (ftp)(http) BW 136.3 Mb (ftp)(http) BW 129.2 Mb (ftp)(http) BW 136.1 Mb (ftp)(http) BW 132.8 Mb (ftp)(http) BW
GSE85337_RAW.tar 2.2 Gb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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