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Series GSE97411 Query DataSets for GSE97411
Status Public on Apr 01, 2020
Title Genomic occupancy of the INO80 complex [ChIP-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We mapped 4 subunits of the INO80 complex using ChIP-seq in HepG2 and Huh7 liver cancer cell lines. We found a subclass of sites occupied by the INO80 ATPase subunit, but not by any accessory subunits that we call 'Autonomous' INO80 sites. These sites are present in both HepG2 and Huh7 cells and are characterized by repressed chromatin. Relief of reprissive histone modifications thorugh EZH2 inhbiition led to the increase in H3K27ac at INO80 targets.
 
Overall design ChIP-seq was performed for INO80 subunits in two cell lines and H3K27ac was mapped in one cell line by ChIP-seq following inhibition of H3K27me3 activity using EPZ-6438. Each experiment was performed twice, and cells were processed for ChIP as previously described (Raab et al 2015), followed by high throughput sequencing.

Please note that the YY1_HepG2 processed data was generated from the ENCODE Accession ENCFF000PSE and ENCFF000PSD with the same pipeline as all the other data (and thus, no GEO sample records were created, and the re-processed data files are included as Series supplementary files).

The author's note: The experiments are quantitative ChIP-seq using drosophila chromatin (Active Motif #53083). We spike this chromatin into each IP, and then use the amount of drosophila chromatin in each sample for calculating the appropriate normalizations between samples. For each experiment there is a bam file corresponding to the sample aligned against hg19 (for the experiment we care about) and against dm3 (for normalizing between sample; GSM2564091-98)
 
Contributor(s) Raab JR, Magnuson T
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Apr 05, 2017
Last update date Apr 02, 2020
Contact name Jesse Raab
E-mail(s) jesse.r.raab@gmail.com
Organization name University of North Carolina Chapel Hill
Department Genetics
Street address 120 Mason Farm Rd
City Chapel Hill
ZIP/Postal code 27599
Country USA
 
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (29)
GSM2564070 INO80_HepG2_A
GSM2564071 INO80_HepG2_B
GSM2564072 INO80_HepG2_C
This SubSeries is part of SuperSeries:
GSE97413 INO80 complex assembly is antagonized by PRC2.
Relations
BioProject PRJNA381706
SRA SRP103082

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
GSE97411_INO80_HepG2_peaks.narrowPeak.filtered.fixed.txt.gz 273.3 Kb (ftp)(http) TXT
GSE97411_INO80_Huh7_peaks.narrowPeak.filtered.fixed.txt.gz 178.0 Kb (ftp)(http) TXT
GSE97411_MCRS1_HepG2_peaks.narrowPeak.filtered.fixed.txt.gz 269.7 Kb (ftp)(http) TXT
GSE97411_MCRS1_Huh7_peaks.narrowPeak.filtered.fixed.txt.gz 70.1 Kb (ftp)(http) TXT
GSE97411_RAW.tar 6.7 Gb (http)(custom) TAR (of BW)
GSE97411_RUVBL1_HepG2_peaks.narrowPeak.filtered.fixed.txt.gz 64.1 Kb (ftp)(http) TXT
GSE97411_RUVBL2_HepG2_peaks.narrowPeak.filtered.fixed.txt.gz 148.7 Kb (ftp)(http) TXT
GSE97411_RUVBL2_Huh7_peaks.narrowPeak.filtered.fixed.txt.gz 38.7 Kb (ftp)(http) TXT
GSE97411_YY1_HepG2_A.sorted.rmdup.depthnorm.bw 87.8 Mb (ftp)(http) BW
GSE97411_YY1_HepG2_B.sorted.rmdup.depthnorm.bw 139.2 Mb (ftp)(http) BW
GSE97411_YY1_HepG2_peaks.narrowPeak.filtered.fixed.txt.gz 445.6 Kb (ftp)(http) TXT
GSE97411_YY1_Huh7_peaks.narrowPeak.filtered.fixed.txt.gz 246.5 Kb (ftp)(http) TXT
GSE97411_dtags_agg.csv.gz 122 b (ftp)(http) CSV
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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