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| Status |
Public on Oct 02, 2022 |
| Title |
Nascent transcription upon interferon-α2 stimulation on human and rhesus macaque lymphoblastoid cell lines |
| Organisms |
Macaca mulatta; Homo sapiens |
| Experiment type |
Other
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| Summary |
Changes in gene transcription regulation are necessary for species to respond to changes in their environment. In particular, host-pathogen dynamics have been observed to entail rapid evolution of genes involved in the host innate immune system. Cytokines such as type I interferon alpha and beta trigger an antiviral cellular state controlled by members of the transcription factor families STAT and IRF. However, it remains poorly understood how gene transcription regulation has been rewired through evolutionary time to achieve species-specific interferon-controlled changes in gene expression. We generated nascent transcription (PRO-seq) datasets to determine the initial transcriptional response on lymphoblastoid cell lines derived from homo sapiens and macaca mulatta upon stimulation with interferon alpha2 to assess species-specific changes in gene regulation.
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| Overall design |
We used lymphoblastoid cell lines derived from two individuals (one male and one female) from homo sapiens and from macaca mulatta; a single replicate per individual, and therefore two samples per species per treatment. PRO-seq datasets were obtained from each individual cell line treated for 1 hour with either BSA (negative control), homo sapiens IFN alpha2, or rhesus macaque IFN alpha2.
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| Contributor(s) |
Ramirez D, Dowell RD |
| Citation(s) |
37885027 |
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| Submission date |
Sep 27, 2022 |
| Last update date |
Nov 13, 2023 |
| Contact name |
Robin D. Dowell |
| E-mail(s) |
robin.dowell@colorado.edu
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| Phone |
303 492 8204
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| Organization name |
University of Colorado Boulder
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| Department |
Molecular, Cellular and Developmental Biology
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| Lab |
Dowell lab
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| Street address |
596 UCB
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| City |
Boulder |
| State/province |
CO |
| ZIP/Postal code |
80309 |
| Country |
USA |
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| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL21120 |
Illumina NextSeq 500 (Macaca mulatta) |
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| Samples (12)
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| GSM6603472 |
PRO-seq, Human LCL female, BSA, 1 hour, rep 1 |
| GSM6603473 |
PRO-seq, Human LCL male, BSA, 1 hour, rep 1 |
| GSM6603474 |
PRO-seq, Human LCL female, hsIFNa2, 1 hour, rep 1 |
| GSM6603475 |
PRO-seq, Human LCL male, hsIFNa2, 1 hour, rep 1 |
| GSM6603476 |
PRO-seq, Human LCL female, rmIFNa2, 1 hour, rep 1 |
| GSM6603477 |
PRO-seq, Human LCL male, rmIFNa2, 1 hour, rep 1 |
| GSM6603478 |
PRO-seq, Rhesus LCL female, BSA, 1 hour, rep 1 |
| GSM6603479 |
PRO-seq, Rhesus LCL male, BSA, 1 hour, rep 1 |
| GSM6603480 |
PRO-seq, Rhesus LCL female, hsIFNa2, 1 hour, rep 1 |
| GSM6603481 |
PRO-seq, Rhesus LCL male, hsIFNa2, 1 hour, rep 1 |
| GSM6603482 |
PRO-seq, Rhesus LCL female, rmIFNa2, 1 hour, rep 1 |
| GSM6603483 |
PRO-seq, Rhesus LCL male, rmIFNa2, 1 hour, rep 1 |
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| Relations |
| BioProject |
PRJNA884834 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE214304_RAW.tar |
2.0 Gb |
(http)(custom) |
TAR (of BED, BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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