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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 16, 2013 |
| Title |
Hi-C, HEK293 siRNA CTCF, replicate two |
| Sample type |
SRA |
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| Source name |
Hi-C, HEK293 siRNA CTCF
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
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| Treatment protocol |
HEK293T cells were transfected with CTCF siRNA oligos using Lipofectamine 2000 according to manufacterure's instructions. Cells were harvested 48hrs later.
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| 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
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| 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).).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| 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:
CTCF_r2_cis.index.txt: hg18
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| Submission date |
Feb 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jesse R Dixon |
| E-mail(s) |
jedixon@salk.edu
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| Organization name |
Salk Institute for Biological Studies
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| Lab |
PBL-D
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| Street address |
10010 N. Torrey Pines Rd.
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE44267 |
Cohesin and CTCF Differentially Affect the Chromatin Architecture and Gene Expression in Human Cells |
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| Relations |
| Reanalyzed by |
GSE87112 |
| SRA |
SRX235599 |
| BioSample |
SAMN01919644 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1081533_CTCF_r2_cis.index.txt.gz |
85.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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