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Sample GSM1055805 Query DataSets for GSM1055805
Status Public on Oct 20, 2013
Title Hi-C H1 hESC
Sample type SRA
 
Source name embryonic stem cells
Organism Homo sapiens
Characteristics treatment: no treat
experiment: Hi-C
antibody: no
restriction enzyme: HindIII
Treatment protocol Untreated or IMR90 cells treated with TNF-α (R&D Systems, 10 ng/mL, 1 hr) or flavopiridol (Sigma, 1 μM for 1 hr for ChIP-seq experiments, and 1 μM for 2 hr for Hi-C experiments) were used.
Growth protocol IMR90 cells were grown as described in: Hawkins, R.D. et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6, 479-91
Extracted molecule genomic DNA
Extraction protocol Hi-C experiments were conducted in biological replicates using HindIII according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).). ChIP-seq protocol can be found from http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf. GRO-seq experiments were performed according to previous publication (Wang, D. et al. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474, 390-4 (2011).).
Libraries were prepared according to Illumina's instruction or cited literatures.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description Raw data for this sample has been previously published with accession code GSM892306
Data processing The paired-end Hi-C reads were mapped to human genome hg18 using BOWTIE. Only first 36 bases were used for mapping when reads is longer. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed.
For GRO-seq, the first round of mapping used the first 36 bases; the unmapped reads were then mapped in two additional iterations using first 30 or 25 bases.
For ChIP-Seq, first 36 bases of each read were used for mapping.
Genome_build: NCBI36
Supplementary_files_format_and_content: Mapped non-redundant reads for GRO-seq and ChIP-seq are in BED format. Mapped non-redundant read pairs for Hi-C are in txt format.
 
Submission date Dec 20, 2012
Last update date Jan 19, 2017
Contact name Fulai Jin
E-mail fxj45@case.edu
Phone 2163681811
Organization name Case Western Reserve University
Lab Fulai Jin
Street address 10900 Euclid Avenue
City Cleveland
State/province OH - OHIO
ZIP/Postal code 44106
Country USA
 
Platform ID GPL11154
Series (1)
GSE43070 Genome-wide Analysis of Chromatin Interactions in Human Cells
Relations
Reanalyzed by GSE93834
SRA SRX212177
BioSample SAMN01832315

Supplementary file Size Download File type/resource
GSM1055805_HiC.H1.rep2.nodup.summary.txt.gz 7.3 Gb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data provided as supplementary file

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