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Series GSE110061 Query DataSets for GSE110061
Status Public on Aug 22, 2020
Title Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution
Organisms Drosophila melanogaster; Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We introduce Chemical-crosslinking Assisted Proximity Capture (CAP-C), a method that utilizes multi-functional chemical crosslinkers with defined physical sizes to directly assess spatial distances between nuclear genomic sequences. CAP-C avoids limitations caused by extensive protein-DNA crosslinking in most in situ methods, and thus generates chromatin contact maps at high resolution with low background noise.
Overall design CAP-C utilizes a multifunctional PAMAM dendrimer platform instead of DNA-bound proteins to crosslink spatially adjacent DNA sequences, followed by restriction digestion and proximal ligation and high-throughput sequencing. We develop this method to examine the chromatin architecture of mouse embryonic stem cell F123, human HCT116 and drosophila S2 cell lines.
Contributor(s) You Q, Cheng AY
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Submission date Feb 02, 2018
Last update date Aug 25, 2020
Contact name Youzhi Cheng
Organization name University of Connecticut Health Center
Department Genetics and Genome Sciences
Street address 400 Farmington Avenue
City Farmington
State/province Connecticut
ZIP/Postal code 06032
Country USA
Platforms (6)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL19132 Illumina NextSeq 500 (Drosophila melanogaster)
Samples (76)
GSM2977170 F123 CAP-C G3 rep1
GSM2977171 F123 CAP-C G3 rep2
GSM2977172 F123 CAP-C G5 rep1
BioProject PRJNA432721
SRA SRP132077

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
GSE110061_BLCAPC-F123-noFormaldehyde_B01_MAPQ1.hic 9.6 Gb (ftp)(http) HIC
GSE110061_BLCAPC-HepG2_B01_MAPQ1.hic 17.8 Gb (ftp)(http) HIC
GSE110061_BLCAPC-HepG2_B01_MAPQ30.hic 16.1 Gb (ftp)(http) HIC
GSE110061_BLCAPC-S2_B01_MAPQ1.hic 911.7 Mb (ftp)(http) HIC
GSE110061_BLCAPC-S2_B01_MAPQ30.hic 838.1 Mb (ftp)(http) HIC
GSE110061_CAPC-BLCAPC_B01_MAPQ1.hic 14.8 Gb (ftp)(http) HIC
GSE110061_CAPC-BLCAPC_B01_MAPQ30.hic 13.0 Gb (ftp)(http) HIC
GSE110061_CAPC-G3_B06_MAPQ1.hic 4.0 Gb (ftp)(http) HIC
GSE110061_CAPC-G3_B06_MAPQ30.hic 3.5 Gb (ftp)(http) HIC
GSE110061_CAPC-G5_B06_MAPQ1.hic 3.5 Gb (ftp)(http) HIC
GSE110061_CAPC-G5_B06_MAPQ30.hic 3.0 Gb (ftp)(http) HIC
GSE110061_CAPC-G7_B06_MAPQ1.hic 4.5 Gb (ftp)(http) HIC
GSE110061_CAPC-G7_B06_MAPQ30.hic 4.0 Gb (ftp)(http) HIC
GSE110061_CAPC-merge_B06_MAPQ1.hic 8.4 Gb (ftp)(http) HIC
GSE110061_CAPC-merge_B06_MAPQ30.hic 7.3 Gb (ftp)(http) HIC
GSE110061_CAPC-merge_S01_MAPQ1.hic 5.2 Gb (ftp)(http) HIC
GSE110061_CAPC-merge_S01_MAPQ30.hic 4.6 Gb (ftp)(http) HIC
GSE110061_CAPC-merge_S02_MAPQ1.hic 5.3 Gb (ftp)(http) HIC
GSE110061_CAPC-merge_S02_MAPQ30.hic 4.6 Gb (ftp)(http) HIC
GSE110061_G5_BLCAPC-CTCF-AID-KO-POLII_B02_MAPQ1.hic 7.4 Gb (ftp)(http) HIC
GSE110061_G5_BLCAPC-CTCF-AID-KO-POLII_B02_MAPQ30.hic 6.6 Gb (ftp)(http) HIC
GSE110061_G5_BLCAPC-CTCF-AID-KO_B02_MAPQ1.hic 8.1 Gb (ftp)(http) HIC
GSE110061_G5_BLCAPC-CTCF-AID-KO_B02_MAPQ30.hic 7.3 Gb (ftp)(http) HIC
GSE110061_G5_BLCAPC-CTCF-AID-POLII_B02_MAPQ1.hic 7.6 Gb (ftp)(http) HIC
GSE110061_G5_BLCAPC-CTCF-AID-POLII_B02_MAPQ30.hic 6.8 Gb (ftp)(http) HIC
GSE110061_G5_BLCAPC-CTCF-AID-WT_B02_MAPQ1.hic 9.3 Gb (ftp)(http) HIC
GSE110061_G5_BLCAPC-CTCF-AID-WT_B02_MAPQ30.hic 8.4 Gb (ftp)(http) HIC
GSE110061_G5_BLCAPC-F123-noFormaldehyde_B02_MAPQ1.hic 3.1 Gb (ftp)(http) HIC
GSE110061_G5_BLCAPC-F123-noFormaldehyde_B02_MAPQ30.hic 2.7 Gb (ftp)(http) HIC
GSE110061_G5_BLCAPC-HCT116-Induction_B01_MAPQ1.hic 7.5 Gb (ftp)(http) HIC
GSE110061_G5_BLCAPC-HCT116-Induction_B01_MAPQ30.hic 6.7 Gb (ftp)(http) HIC
GSE110061_G5_BLCAPC-HCT116-WT_B01_MAPQ1.hic 3.2 Gb (ftp)(http) HIC
GSE110061_G5_BLCAPC-HCT116-WT_B01_MAPQ30.hic 2.8 Gb (ftp)(http) HIC
GSE110061_G7_BLCAPC-F123-noFormaldehyde_B01_MAPQ1.hic 3.5 Gb (ftp)(http) HIC
GSE110061_G7_BLCAPC-F123-noFormaldehyde_B01_MAPQ30.hic 3.1 Gb (ftp)(http) HIC
GSE110061_G9_BLCAPC-F123-noFormaldehyde_B01_MAPQ1.hic 6.4 Gb (ftp)(http) HIC
GSE110061_G9_BLCAPC-F123-noFormaldehyde_B01_MAPQ30.hic 5.8 Gb (ftp)(http) HIC
GSE110061_RAW.tar 439.8 Gb (http)(custom) TAR (of BIGWIG, HIC, NARROWPEAK)
GSE110061_README.txt 6.5 Kb (ftp)(http) TXT
GSE110061_in-situ_B02_MAPQ1.hic 12.0 Gb (ftp)(http) HIC
GSE110061_in-situ_B02_MAPQ30.hic 10.7 Gb (ftp)(http) HIC
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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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