GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE54846 Query DataSets for GSE54846
Status Public on Sep 15, 2014
Title RNA-seq from control and macroH2A1-depleted IMR90 primary human lung fibroblasts
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The histone variant macroH2A1 and the poly(ADP-ribose) polymerase PARP-1 both regulate gene transcription by modulating chromatin structure and function. Of the two macroH2A1 splice variants, macroH2A1.1 and macroH2A1.2, the former is often suppressed in cancer and has the unique ability to interact with poly(ADP-ribose). Using ChIP-seq in primary lung fibroblasts, we demonstrate that macroH2A1 is incorporated into either of two spatially and functionally distinct types of chromatin; the first is marked by H3 K27 trimethylation, while the second contains a set of nine histone acetylations. MacroH2A1-regulated genes are involved in cancer progression are specifically found in macroH2A1-containing acetylated chromatin. Through the recruitment of PARP-1, macroH2A1.1 promotes the acetylation of H2B K12 and K120 which plays a key role in the regulation of macroH2A1 target genes in primary cells. The macroH2A1/PARP-1 pathway regulating H2B K12 and K120 acetylation is disrupted in cancer cells, in part, explaining macroH2A1’s role in cancer suppression.
Overall design Three biological replicates of RNA-seq from cells expressing shRNA directed against macroH2A1 or luciferase as a control
Contributor(s) Gamble MJ, Chen H
Citation(s) 25306110
Submission date Feb 10, 2014
Last update date May 15, 2019
Contact name Matthew Jon Gamble
Organization name Albert Einstein College of Medicine
Department Molecular Pharmacology
Lab Gamble Lab
Street address 1300 Morris Park Ave / Golding 203
City Bronx
State/province NY
ZIP/Postal code 10461
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (6)
GSM1325074 Luc KD replicate 1
GSM1325075 Luc KD replicate 2
GSM1325076 Luc KD replicate 3
This SubSeries is part of SuperSeries:
GSE54847 Exploring the role of macroH2A1 in transcription regulation in IMR90 primary human lung fibroblasts with RNA-seq and ChIP-seq
BioProject PRJNA237809
SRA SRP037550

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
GSE54846_130529.DESeq.120813.combined-htseq-Luc123-m1_123.HGNC.protein_coding.rsgt20.txt.gz 708.6 Kb (ftp)(http) TXT
GSE54846_RAW.tar 1.1 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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