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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
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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.
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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. https://github.com/dpryan79/Misc/blob/master/InternalBarcodes/demultiplex_relacs.py
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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 |
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Submission date |
Feb 22, 2018 |
Last update date |
Mar 27, 2019 |
Contact name |
Thomas Manke |
E-mail(s) |
manke@ie-freiburg.mpg.de
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Organization name |
Max Planck Institute of Immunobiology and Epigenetics
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Street address |
Stuebeweg 51
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City |
Freiburg |
ZIP/Postal code |
79108 |
Country |
Germany |
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Platforms (5)
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GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
GPL21290 |
Illumina HiSeq 3000 (Homo sapiens) |
GPL21493 |
Illumina HiSeq 3000 (Mus musculus) |
GPL24632 |
Illumina HiSeq 2000 (Drosophila melanogaster; Homo sapiens; Mus musculus) |
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Samples (44)
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GSM3019932 |
RELACS HepG2 H3K36me3 |
GSM3019933 |
RELACS HepG2 H3K9me3 |
GSM3019934 |
RELACS HepG2 H3K27me3 |
GSM3019935 |
RELACS HepG2 CTCF |
GSM3019936 |
RELACS HepG2 p300 |
GSM3019937 |
RELACS HepG2 input |
GSM3019938 |
Traditional HepG2 H3K27ac |
GSM3019939 |
Traditional HepG2 H3K4me3 |
GSM3019940 |
TraditionalHepG2 H3K4me1 |
GSM3019941 |
Traditional HepG2 H3K36me3 |
GSM3019942 |
Traditional HepG2 H3K9me3 |
GSM3019943 |
Traditional HepG2 H3K27me3 |
GSM3019944 |
Traditional HepG2 CTCF |
GSM3019945 |
Traditional HepG2 p300 |
GSM3019946 |
Traditional HepG2 input |
GSM3019947 |
RELACS HepG2 H3K4me3 10,000 |
GSM3019948 |
RELACS HepG2 H3K27me3 10,000 |
GSM3019949 |
RELACS HepG2 CTCF 10,000 |
GSM3019950 |
RELACS HepG2 input 10,000 |
GSM3019951 |
RELACS HepG2 H3K4me3 1000 |
GSM3019952 |
RELACS HepG2 H3K27me3 1000 |
GSM3019953 |
RELACS HepG2 CTCF 1000 |
GSM3019954 |
RELACS HepG2 input 1000 |
GSM3019955 |
RELACS HepG2 H3K4me3 100 |
GSM3019956 |
RELACS HepG2 H3K27me3 100 |
GSM3019957 |
RELACS HepG2 CTCF 100 |
GSM3019958 |
RELACS HepG2 input 100 |
GSM3019959 |
Mouse H3K27ac (16 tissues) |
GSM3019960 |
Mouse H3K36me3 (16 tissues) |
GSM3019961 |
Mouse H3K27me3 (16 tissues) |
GSM3019962 |
Mouse input (16 tissues) |
GSM3019963 |
Cross contamination control |
GSM3380021 |
Mouse RELACS CTCF (16 tissues) |
GSM3380022 |
RELACS CTCF (4 replicates), no UMI |
GSM3380023 |
RELACS CTCF (4 replicates), 2 base UMI |
GSM3380024 |
RELACS CTCF (4 replicates), 3 base UMI |
GSM3380025 |
RELACS CTCF (4 replicates), 4 base UMI |
GSM3380026 |
RELACS Input (4 replicates), no UMI |
GSM3380027 |
RELACS Input (4 replicates), 2 base UMI |
GSM3380028 |
RELACS Input (4 replicates), 3 base UMI |
GSM3380029 |
RELACS Input (4 replicates), 4 base UMI |
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Relations |
BioProject |
PRJNA435556 |
SRA |
SRP133279 |
Supplementary file |
Size |
Download |
File type/resource |
GSE111000_CTCF_narrow_peaks.narrowPeak.gz |
546.7 Kb |
(ftp)(http) |
NARROWPEAK |
GSE111000_CviKI_1.bw |
227.5 Mb |
(ftp)(http) |
BW |
GSE111000_CviKI_1.fltrdChr.bed.gz |
233.9 Mb |
(ftp)(http) |
BED |
GSE111000_CviKI_1.mm10.bw |
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 |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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