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Sample GSM1081530 Query DataSets for GSM1081530
Status Public on Dec 16, 2013
Title Hi-C, HEK293 siRNA Control, replicate one
Sample type SRA
 
Source name Hi-C, HEK293 siRNA Control
Organism Homo sapiens
Characteristics cell line: HEK293T
Treatment protocol HEK293T cells were transfected with control siRNA oligos using Lipofectamine 2000 according to manufacterure's instructions. Cells were harvested 48hrs later.
Growth protocol Cells were grown in DMEM supplemented with 0.2mM L-glutamine, 100 U/mL penicillin, 100 mg/mL streptomycin, and 10% fetal calf serum at 37°C and 5% CO2
Extracted molecule genomic DNA
Extraction protocol Hi-C experiments were conducted 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).).
Sequencing libraries were constructed 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).).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Data processing Library strategy: Hi-C
fastq: Illumina's HiSeq Control Software
Hi-C reads were aligned as single end reads using BWA with default parameters. Uniquely mapping reads were manually paired using in an in house pipeline. PCR duplicate reads were removed using Picard MarkDuplicates.
RNA-seq data were mapped as paired-end reads using tophat with the following parameters: -g 1 -p 12 --solexa1.3-quals --library-type fr-firststrand --segment-length 25 --bowtie1
RNA-seq bigWig files were generated through an in house pipeline that includes performing trimmed mean of M (TMM) normalization (Robinson et al. Genome Biology 2010)
ChIP-seq data were mapping with bowtie using the following parameters: -v 3 -m 1 --best --strata -S --time -p 8. Data was filtered for uniquely mapping reads. PCR duplicates were removed using Picard MarkDuplicates
ChIP-seq bigWig files were generated through an in house pipeline
Genome_build: hg18
Supplementary_files_format_and_content: ChIP-seq and RNA-seq processed files are in bigWig format. As the RNA-seq experiment was strand specific, bigWig files for both the positive and negative strands are included
Supplementary_files_format_and_content: Hi-C processed files are in a modified bed format. Each row lists the chromosome and the start and end coordiates of two interacting bins as well as the normalized interaction frequency between these two bins
Supplementary_files_format_and_content: Processed mRNA-seq data include information for each gene and its count and rpkm values. Each line includes chromosome, start position, end position, strand, gene name, read counts, and rpkm values
Genome Build:
CTRL_r1_cis.index.txt: hg18
 
Submission date Feb 12, 2013
Last update date Sep 20, 2016
Contact name Jesse R Dixon
E-mail jedixon@salk.edu
Organization name Salk Institute for Biological Studies
Lab PBL-D
Street address 10010 N. Torrey Pines Rd.
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL11154
Series (1)
GSE44267 Cohesin and CTCF Differentially Affect the Chromatin Architecture and Gene Expression in Human Cells
Relations
Reanalyzed by GSE87112
SRA SRX235596
BioSample SAMN01919641

Supplementary file Size Download File type/resource
GSM1081530_CTRL_r1_cis.index.txt.gz 82.3 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data provided as supplementary file

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