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Sample GSM1826481 Query DataSets for GSM1826481
Status Public on Sep 01, 2015
Title Hi-C, SK-N-SH, Replicate 1
Sample type SRA
 
Source name SK-N-SH
Organism Homo sapiens
Characteristics cell line: SK-N-SH
Treatment protocol Cells crosslinked for 10 minutes at room temperature with 1% formadehyde. Quencing was performed with 0.125M glycine for 5 minutes are room temperature
Growth protocol Cells cultured in RPMI media supplemented with 10% FBS
Extracted molecule genomic DNA
Extraction protocol Hi-C and library prep were performed as previously described (Dixon et al., Nature. 2012. PMID:22495300).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Data processing Hi-C reads were mapped to hg19 using BWA-MEM. Reads were aligned as single ends, and read pairs are then re-constructed after mapping.
Unmapped reads were filtered out and PCR duplicate reads were removed with PicardTools MarkDuplicates.
Contact matrices were constructed at 40kb resolution and normalized with HiCNorm (Hu, M. et al., Bioinformatics. 2012. PMID: 23023982).
Topologically associated domains (“TADs”) were identified based on Directionality Index (“DI”) as described previously (Dixon et al., Nature. 2012. PMID: 22495300), with one exception: DI was calculated using a sliding window of 300 kb upstream/downstream of the view point.
Genome_build: hg19
 
Submission date Jul 18, 2015
Last update date May 15, 2019
Contact name David Gorkin
E-mail(s) dgorkin@ucsd.edu
Organization name Ludwig Institute for Cancer Research
Lab Bing Ren
Street address 9500 Gilman Dr. CMM-East 2071
City La Jolla
State/province California
ZIP/Postal code 92093
Country USA
 
Platform ID GPL16791
Series (1)
GSE71072 SK-N-SH Hi-C
Relations
BioSample SAMN03879914
SRA SRX1100381

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data is available on Series record

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