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| Status |
Public on Oct 06, 2014 |
| Title |
Hi-C HindIII T60 |
| Sample type |
SRA |
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| Source name |
Breast cancer cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Breast cancer cell line T47D-MTVL
treatment: progestin R5020-stimulated
time (minutes): 60
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| 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
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| 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
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| 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
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample 3
HiC
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| 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.
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| Submission date |
Dec 18, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Miguel Beato |
| E-mail(s) |
miguel.beato@crg.eu
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| Organization name |
CRG
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| Street address |
Aiguader 88
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| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE53463 |
Distinct structural transitions of chromatin topological domains coordinate hormone-induced gene regulation |
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| Relations |
| BioSample |
SAMN02464027 |
| SRA |
SRX395601 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1294039_hindIII_T60_100kb.mat.txt.gz |
50.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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