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| Status |
Public on Oct 30, 2020 |
| Title |
SNU484_Capture-C |
| Sample type |
SRA |
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| Source name |
gastric cancer cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: SNU484
cell type: gastric cancer cell line
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Capture-C probes at CCNE1 promoter regions were designed using CapSequm. Approximately 1 × 10e7 cells were crosslinked by 2% formaldehyde, followed by lysis, homogenization, DpnII digestion, ligation and de-crosslinking. DNA was sonicated using a Covaris to 150–200 bp to produce DNA suitable for oligo capture. Three micrograms of sheared DNA was used for sequencing library preparation (New England Biolabs). The promoter sequence of CCNE1 was double captured by sequential hybridization to customized biotinylated oligos (IDT, Supplementary Table 14) and enrichment with Dynabeads (LifeTech). Captured DNA was sequenced on the Illumina HiSeq 3000 instrument with the 2x150 bp configuration.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
Capture-C in SNU484
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| Data processing |
Library strategy: Capture-C
Pre-processing of raw reads was performed to remove adaptor sequences (trim_galore, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and overlapping reads were merged using FLASH. In order to achieve short read mapping to the hg19 reference genome, the resulting pre-processed reads were then in-silico digested with DpnII and aligned using Bowtie (using p1, m2, best and strata settings). Aligned reads were processed using Capture-C analyser to (i) remove PCR duplicates, and (ii) classify sub fragments as ‘capture’ if they were contained within the capture fragment; ‘proximity exclusion’ if they were within 1 Kb on either side of the capture fragment; or ‘reporter’ if they were outside of the ‘capture’ and ‘proximity exclusion’ regions. We additionally used the r3Cseq package on the capture and reporter fragments to identify significant interactions of the viewpoint against a scaled background (q-value <0.05, FDR).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Space-delimited text files with columns starting with chromosome, start, end, width, nReads, RPMs, z, p.value and q.value.
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| Submission date |
Oct 11, 2018 |
| Last update date |
Oct 30, 2020 |
| Contact name |
Wen Fong Ooi |
| E-mail(s) |
[email protected]
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| Organization name |
Genome Institute of Singapore
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| Street address |
60 Biopolis
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| City |
Singapore |
| ZIP/Postal code |
470110 |
| Country |
Singapore |
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| Platform ID |
GPL21290 |
| Series (2) |
| GSE121136 |
Genomic and Epigenomic EBF1 Alterations Modulate TERT Expression in Gastric Cancer [Capture-C] |
| GSE121140 |
Genomic and Epigenomic EBF1 Alterations Modulate TERT Expression in Gastric Cancer |
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| Relations |
| BioSample |
SAMN10232013 |
| SRA |
SRX4863829 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3426715_SNU484_P119.txt.gz |
2.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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