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Sample GSM4411228 Query DataSets for GSM4411228
Status Public on Sep 12, 2020
Title 26APR16-PacBio-HelaS3-unsyn
Sample type SRA
Source name DpnII MC-3C on Asynchronious cells
Organism Homo sapiens
Characteristics protocol: MC-3C
enzyme: DpnII
cell line: HelaS3
Growth protocol Hela S3 cells were grown in DMEM media supplemented with 10% FBS and 1% Pen/Strep
Extracted molecule genomic DNA
Extraction protocol For each MC-3C library 5 Million cells were crosslinked
MC-3C was performed as described in detail in supplemental methods.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model PacBio RS II
Data processing Library strategy: MC-3C
reads with a quality threshold over 80 were selected
reads were virtually cut at the sequence sites recognized by DpnII (GATC
cut reads were mapped using bwa-mem
cut reads had to align at least 85% to the DpnII Genomic fragment to be assigned
combined all replicates as final output
Genome_build: hg19
Supplementary_files_format_and_content: table with all interactions from c-walks represented as pairwise interactions (tab seperated)
Submission date Mar 13, 2020
Last update date Sep 12, 2020
Contact name Bastiaan Dekker
Organization name University of Massachusetts Medical School
Department Systems Biology
Lab Dekker lab
Street address 368 Plantation street
City Worcester
State/province Massachusetts
ZIP/Postal code 01605
Country USA
Platform ID GPL21311
Series (1)
GSE146945 Multi-contact 3C data reveal that the human genome is largely unentangled
BioSample SAMN14374607
SRA SRX7909614

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

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