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| Status |
Public on Aug 24, 2020 |
| Title |
MGH1904-sb_HiC |
| Sample type |
SRA |
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| Source name |
Colon tumor
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Colon tumor
biological sample: MGH1904
treatment: NA
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
In situ HiC was performed as described previously (Rao et al., 2014). In brief, crosslinked cells or tumor were thawed on ice in HiC lysis buffer. Tissue samples were mechanically disrupted with the Biomasher tissue grinder (Kimble Chase). Tissue and cell line samples were permeabilized in 0.5% SDS at 37 degrees, quenched with Triton X100 and chromatin was digested with 100-200U MboI at 37 degrees overnight. Nuclei were then pelleted, ends were marked with biotin-14-dATP (ThermoFisher 19524016) and chromatin was ligated for 5 hours by T4 DNA ligase (M0202). Samples were treated with proteinase K at 55 degrees for 30 minutes and cross-links were reversed at 68 degrees overnight. DNA was ethanol precipitated and sheared on a Covaris LE220 as per Rao et al., 2014. DNA was cleaned up via AMPure XP beads (Beckman Coulter, A63881) and quantified by Qubit dsDNA High Sensitivity Assay (Life Technologies, Q32854). Samples were bound to Dynabeads MyOne Streptavidin T1 beads (Life technologies, 65602) and washed. End repair, dATP attachment and adapter ligation was performed. Final PCR amplification was performed using barcoded sequencing primers and PCR. Libraries were purified using AMPure XP beads and sequenced on either a NextSeq500 (150 cycle kit) or the HiSeq2500 (high output; 200 cycle kit).
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Data were controlled for quality, mapped to the reference genome (hg19) and converted into interaction matrices using HiC-Pro (Servant et al., 2015). Within sample normalization was performed using the Iterative Correction and Eigenvector decomposition (ICE) method (Imakaev et al., 2012).
processed data files format and content: HiC Interaction matrix files (.matrix). As provided by the HiCPro pipeline. A matrix, stored as standard triplet sparse format (i.e. list format). Based on the observation that a contact map is symmetric and usually sparse, only non-zero values are stored for half of the matrix.
processed data files format and content: HiC all valid interaction read pairs (allValidPairs). As provided by the HiCPro pipeline. Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size.
Genome_build: hg19
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| Submission date |
Jul 08, 2019 |
| Last update date |
Aug 29, 2020 |
| Contact name |
Alejandro Reyes |
| Organization name |
Novartis Institutes For BioMedical Research
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| Department |
Data Sciences
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| Street address |
Fabrikstrasse 22
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| City |
Basel |
| ZIP/Postal code |
4056 |
| Country |
Switzerland |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE133928 |
A topological atlas reveals layers of genome reorganization in colorectal cancer |
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| Relations |
| BioSample |
SAMN12230119 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3930287_MGH1904-sb_100000_iced.matrix.gz |
156.0 Mb |
(ftp)(http) |
MATRIX |
| GSM3930287_MGH1904-sb_40000_iced.matrix.gz |
204.6 Mb |
(ftp)(http) |
MATRIX |
| GSM3930287_MGH1904-sb_hic_allValidPairs.txt.gz |
1.4 Gb |
(ftp)(http) |
TXT |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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