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Series GSE99177 Query DataSets for GSE99177
Status Public on Aug 24, 2017
Title ChIP-seq analysis of dCas9 chromatin occupancy by dCas9/sgRNA-mediated CAPTURE
Organisms Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Cis-regulatory elements (CREs) are commonly recognized by correlative chromatin features, yet the molecular composition of the vast majority of CREs in chromatin remains unknown. Here we describe a CRISPR affinity purification in situ of regulatory elements (CAPTURE) approach to unbiasedly identify locus-specific chromatin-regulating protein complexes and long-range DNA interactions. Using an in vivo biotinylated endonuclease-deficient Cas9 protein and sequence-specific guide RNAs, we show high-resolution and selective isolation of chromatin interactions at a single copy genomic locus. Purification of human telomeres using CAPTURE identifies known and new telomeric factors. In situ capture of individual constituents of the enhancer cluster controlling human β-globin genes establishes evidence for composition-based hierarchical organization of enhancer structure. Furthermore, unbiased analysis of chromatin interactions at disease-associated cis-elements and developmentally controlled super-enhancers reveals spatial features causally regulate gene transcription. Thus, comprehensive analysis of locus-specific regulatory composition provides mechanistic insight into genome structure and function in development and disease.
Overall design ChIP-seq was performed to determine the chromatin occupancy of biotinylated dCas9 in cells expressing target-specific sgRNAs or the non-targeting sgRNA (sgGal4).
Contributor(s) Liu X, Zhang Y, Xu J
Citation(s) 28841410
Submission date May 22, 2017
Last update date Jul 25, 2021
Contact name Jian Xu
Phone 9015955208
Organization name St. Jude Children's Research Hospital
Department Pathology
Street address 262 Danny Thomas Place, MS 345
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (61)
GSM2635188 CAPTURE-ChIP-seq_K562_sgHS1-rep1
GSM2635189 CAPTURE-ChIP-seq_K562_sgHS1-rep2
GSM2635190 CAPTURE-ChIP-seq_K562_sgHS2-rep1
This SubSeries is part of SuperSeries:
GSE88817 In situ CAPTURE of chromatin interactions by biotinylated dCas9
BioProject PRJNA387472
SRA SRP107798

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
GSE99177_CAPTURE-ChIP-seq_K562_sg3HS1_vs_sgGal4_merged.txt.gz 344.2 Kb (ftp)(http) TXT
GSE99177_CAPTURE-ChIP-seq_K562_sgHBB-sg2_vs_sgGal4_merged.txt.gz 157.1 Kb (ftp)(http) TXT
GSE99177_CAPTURE-ChIP-seq_K562_sgHBB_vs_sgGal4_merged.txt.gz 161.4 Kb (ftp)(http) TXT
GSE99177_CAPTURE-ChIP-seq_K562_sgHBD-1kb_vs_sgGal4_merged.txt.gz 322.8 Kb (ftp)(http) TXT
GSE99177_CAPTURE-ChIP-seq_K562_sgHBG-sg2_vs_sgGal4_merged.txt.gz 197.3 Kb (ftp)(http) TXT
GSE99177_CAPTURE-ChIP-seq_K562_sgHBG_vs_sgGal4_merged.txt.gz 252.8 Kb (ftp)(http) TXT
GSE99177_CAPTURE-ChIP-seq_K562_sgHS1-5_vs_sgGal4_merged.txt.gz 606.7 Kb (ftp)(http) TXT
GSE99177_CAPTURE-ChIP-seq_K562_sgHS1-sg2_vs_sgGal4_merged.txt.gz 276.4 Kb (ftp)(http) TXT
GSE99177_CAPTURE-ChIP-seq_K562_sgHS1_vs_sgGal4_merged.txt.gz 125.8 Kb (ftp)(http) TXT
GSE99177_CAPTURE-ChIP-seq_K562_sgHS2-sg2_vs_sgGal4_merged.txt.gz 237.8 Kb (ftp)(http) TXT
GSE99177_CAPTURE-ChIP-seq_K562_sgHS2_vs_sgGal4_merged.txt.gz 197.1 Kb (ftp)(http) TXT
GSE99177_CAPTURE-ChIP-seq_K562_sgHS3-sg2_vs_sgGal4_merged.txt.gz 176.8 Kb (ftp)(http) TXT
GSE99177_CAPTURE-ChIP-seq_K562_sgHS3_vs_sgGal4_merged.txt.gz 270.2 Kb (ftp)(http) TXT
GSE99177_CAPTURE-ChIP-seq_K562_sgHS4-sg2_vs_sgGal4_merged.txt.gz 187.2 Kb (ftp)(http) TXT
GSE99177_CAPTURE-ChIP-seq_K562_sgHS4_vs_sgGal4_merged.txt.gz 318.4 Kb (ftp)(http) TXT
GSE99177_CAPTURE-ChIP-seq_K562_sgHS5-sg2_vs_sgGal4_merged.txt.gz 207.0 Kb (ftp)(http) TXT
GSE99177_CAPTURE-ChIP-seq_K562_sgHS5_vs_sgGal4_merged.txt.gz 592.3 Kb (ftp)(http) TXT
GSE99177_RAW.tar 5.7 Gb (http)(custom) TAR (of BED, WIG)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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