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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