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Series GSE111000 Query DataSets for GSE111000
Status Public on Mar 06, 2018
Title Ultra-parallel ChIP-seq by barcoding of intact nuclei
Organisms Drosophila melanogaster; Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is an invaluable tool for mapping chromatin-associated proteins. Processing of samples still remains largely individual and labor-intensive, hindering the assay throughput and comparability across samples.
Here we present a novel method for ultra-parallelized high-throughput ChIP-seq for the systematic mapping of histone modifications and transcription factors. The method, called RELACS (Restriction Enzyme-based Labeling of Chromatin in Situ), barcodes chromatin within intact nuclei extracted from different tissutal sources.
Barcoded nuclei are pooled and processed within the same ChIP, for maximal comparability and drastical workload reduction. The choice of user-friendly, straightforward, enzymatic steps for chromatin fragmentation and barcoding makes RELACS particularly suitable for implementation in any clinical laboratory settings, for scarce samples, and large-scale studies.
Overall design RELACS ChIP-seq has been firstly validated using HepG2 cells and compared with traditional sonication-based protocol. For this purpose, ChIP against six histone modifications and two transcription factors has been performed. 20 parallel technical replicates were investigated for RELACS within the same ChIP.
A sensitivity test for RELACS has been also performed. For this, seven technical replicates containing 10,000, 1,000 and 100 cells each have been barcoded and merged to be processed in three separated ChIPs (containing 7x10,000, 7x1,000, 7x100 cells respectively). ChIP sensitivity has been investigated for H3K4me3, H3K27me3 and CTCF.
To demonstrate ChIP parallelization we applicated RELACS for barcoding 8 separate organs extracted from two mice and processed within the same ChIP. For mouse experiments H3K27ac, H3K36me3, H3K27me3 ChIPs (and input controls) have been performed.
Contributor(s) Arrigoni L, Al-Hasani H, Ramirez F, Panzeri I, Ryan DP, Santacruz D, Kress N, Pospisilik A, Boenisch U, Manke T
Citation(s) 30534606
Submission date Feb 22, 2018
Last update date Mar 27, 2019
Contact name Thomas Manke
Organization name Max Planck Institute of Immunobiology and Epigenetics
Street address Stuebeweg 51
City Freiburg
ZIP/Postal code 79108
Country Germany
Platforms (5)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (44)
GSM3019929 RELACS HepG2 H3K27ac
GSM3019930 RELACS HepG2 H3K4me3
GSM3019931 RELACS HepG2 H3K4me1
BioProject PRJNA435556
SRA SRP133279

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
GSE111000_CTCF_narrow_peaks.narrowPeak.gz 546.7 Kb (ftp)(http) NARROWPEAK 227.5 Mb (ftp)(http) BW
GSE111000_CviKI_1.fltrdChr.bed.gz 233.9 Mb (ftp)(http) BED 204.9 Mb (ftp)(http) BW
GSE111000_CviKI_1.mm10.fltrdChr.bed.gz 208.0 Mb (ftp)(http) BED
GSE111000_H3K27ac_narrow_peaks.narrowPeak.gz 1.7 Mb (ftp)(http) NARROWPEAK
GSE111000_H3K4me3_narrow_peaks.narrowPeak.gz 1.2 Mb (ftp)(http) NARROWPEAK
GSE111000_RAW.tar 1.0 Gb (http)(custom) TAR (of BW)
GSE111000_RELACS_H3K27me3.filtered.histoneHMM-regions.gff.gz 332.5 Kb (ftp)(http) GFF
GSE111000_RELACS_H3K36me3.filtered.histoneHMM-regions.gff.gz 255.4 Kb (ftp)(http) GFF
GSE111000_RELACS_H3K4me1.filtered.histoneHMM-regions.gff.gz 504.8 Kb (ftp)(http) GFF
GSE111000_RELACS_H3K9me3.filtered.histoneHMM-regions.gff.gz 1.5 Mb (ftp)(http) GFF
GSE111000_Traditional_CTCF.filtered.BAM_peaks.narrowPeak.gz 295.9 Kb (ftp)(http) NARROWPEAK
GSE111000_Traditional_H3K27ac.filtered.BAM_peaks.narrowPeak.gz 1.7 Mb (ftp)(http) NARROWPEAK
GSE111000_Traditional_H3K27me3.filtered.histoneHMM-regions.gff.gz 251.2 Kb (ftp)(http) GFF
GSE111000_Traditional_H3K36me3.filtered.histoneHMM-regions.gff.gz 347.6 Kb (ftp)(http) GFF
GSE111000_Traditional_H3K4me1.filtered.histoneHMM-regions.gff.gz 1.0 Mb (ftp)(http) GFF
GSE111000_Traditional_H3K9me3.filtered.histoneHMM-regions.gff.gz 626.7 Kb (ftp)(http) GFF
GSE111000_Traditional_p300.filtered.BAM_peaks.narrowPeak.gz 4.2 Kb (ftp)(http) NARROWPEAK
GSE111000_p300_narrow_peaks.narrowPeak.gz 16.1 Kb (ftp)(http) NARROWPEAK
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