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Sample GSM1294039 Query DataSets for GSM1294039
Status Public on Oct 06, 2014
Title Hi-C HindIII T60
Sample type SRA
Source name Breast cancer cell line
Organism Homo sapiens
Characteristics cell line: Breast cancer cell line T47D-MTVL
treatment: progestin R5020-stimulated
time (minutes): 60
Treatment protocol For the experiments, cells were plated in RPMI medium without phenol red supplemented with 10% dextran-coated charcoal-treated FBS and 48 hr later medium was replaced by fresh medium without serum. After 1 day in serum-free conditions, cells were incubated with R5020 (10 nM) 0 and 60 minutes
Growth protocol Cells were routinely grown in RPMI 1640 medium supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100 mg/ml streptomycin
Extracted molecule genomic DNA
Extraction protocol After hormone treatment, the medium was replaced by medium containing 1% formaldehyde and incubated 10 min for cross-linking. The reaction was stop by adding 125 mM glycine. Hi-C librarires were prepared as described in Lieberman-Aiden et al. (Science, 2009).
Lieberman-Aiden et al., 2009
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
Description Sample 3
Data processing Library strategy: Hi-C
Basecalls performed using Illumina pipeline version 1.4.0
ChIP-Seq Single-end reads were processed by aligning to the reference human genome (GRCh37/hg19) using Bowtie v1.0.0. ChIP-seq signals were summed in windows of 100 Kb. Summed reads were normalized for sequencing depth and divided by the corresponding signal obtained for an input DNA of T47D cells to determine the normalized signal over input enrichment/depletion. Homer (Hypergeometric Optimization of Motif EnRichment) v4.3 was used to find regions of significance enrichment using an input as a control.
HiC Paired-end reads were processed by first aligning to the reference human genome (GRCh37/hg19) using BWA. Reads filtered from analysis include those that were not uniquely mapped, mapped more than 500 bp from relevant restriction sites, had bad sequence quality (e.g. 40% or more of the bases with Sanger PHRED quality ≤ 2) or bad BWA mapping quality (≤ 20), or were located in regions classified to have exceptionally high sequence depth (top 0.1%) by the 1000 Genomes project’s data. To offset bias introduced by PCR amplification of the sequencing library, only one of the duplicated pairs were used for subsequent analyses. Datasets were used to generate contact matrices at 100 Kb.
RNA-Seq Paired-end reads were mapped using GEM mRNA Mapping Pipeline (v1.7) using last Gencode Annotation version 18, which followed specific steps: 1) Map reads to genome reference index (including chromosme 1 to X) with maximum mismatch ratio of 0.06 and base quality threshold of 26. 2) Map reads to a transcriptome index generated from previous reference index using same options as step 1. 3) Create de-novo trasncriptome index and map again the reads to this index using maximum mismatch ratio of 0.04, minimmum split size of 15 bp and maximmum of 500000 bp. 4) Map reads again to de-novo transcriptome index created using same options as step 1. 5) Merge mappings created and pair alignments using with base quality threshold of 26 and maximmum insertion size of 500000 bp. As a result BAM alignment files were obtained and used to generate strand-specific genome-wide normalized profiles using RSeQC3 software. Exon quantifications summarized by per-genes for expression level determination were obtained either as raw read counts and reads per kilobase per milion mapped reads (RPKM) using Flux Capacitor.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq data files are peak results “TSV” files with genomic coordinates of peaks. HiC data files are whole genome “TSV” matrices. RNA-Seq data file is a “TSV” table which summarizes read counts per genes.
Submission date Dec 18, 2013
Last update date Oct 07, 2014
Contact name Miguel Beato
Organization name CRG
Street address Aiguader 88
City Barcelona
ZIP/Postal code 08003
Country Spain
Platform ID GPL11154
Series (1)
GSE53463 Distinct structural transitions of chromatin topological domains coordinate hormone-induced gene regulation
BioSample SAMN02464027
SRA SRX395601

Supplementary file Size Download File type/resource
GSM1294039_hindIII_T60_100kb.mat.txt.gz 50.1 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data provided as supplementary file

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