GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE84259 Query DataSets for GSE84259
Status Public on Jan 03, 2017
Title TRIM28 controls a gene regulatory network based on endogenous retroviruses in human neural progenitor cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Endogenous retroviruses (ERVs), which make up 8% of the human genome, have been proposed to participate in the control of gene regulatory networks. In this study, we find a region- and developmental stage-specific expression pattern of ERVs in the developing human brain, which is linked to a transcriptional network based on ERVs. We demonstrate that almost ten thousand, primarily primate-specific ERVs, act as docking platforms for the epigenetic co-repressor protein TRIM28 in human neural progenitor cells, which results in the establishment of local heterochromatin. Thereby, TRIM28 represses ERVs and consequently regulates the expression of neighboring genes. These results uncover a gene regulatory network based on ERVs that participates in control of gene expression of protein-coding transcripts important for brain development.
Overall design ChIP-seq; TRIM28 and H3K9me3 in hNPCs, normalized to total input. RNA-seq; WT and TRIM28-KD two hNPCs cell lines. One fetal derived (Sai2) and one iPS-derived (AF22) , three replicates each treatment and each cell line. RNA-seq of the fetal brain.
Contributor(s) Brattås PL, Jönsson M, Fasching L, Nelander Wahlestedt J, Shahsavani M, Falk R, Falk A, Jern P, Parmar M, Jakobsson J
Citation(s) 28052240
Submission date Jul 11, 2016
Last update date May 15, 2019
Contact name Per Brattas
Organization name Lund University
Lab Clinical Genomics
Street address Sölvegatan 17
City Lund
ZIP/Postal code 221 84
Country Sweden
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (34)
GSM2230406 TRIM28-KD_Sai-1
GSM2230407 TRIM28-KD_Sai-2
GSM2230408 TRIM28-KD_Sai-3
BioProject PRJNA328486
SRA SRP078262

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource 74.2 Mb (ftp)(http) TXT
GSE84259_RAW.tar 1.2 Mb (http)(custom) TAR (of BED) 64.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap