|
| 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
Other
|
| 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.
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| 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.
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| Contributor(s) |
You Q, Cheng AY |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| 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 |
| |
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| Platforms (6)
|
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL19132 |
Illumina NextSeq 500 (Drosophila melanogaster) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (76)
|
|
| Relations |
| BioProject |
PRJNA432721 |
| SRA |
SRP132077 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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