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Sample GSM3058263 Query DataSets for GSM3058263
Status Public on Mar 01, 2019
Title colon epthelial cells input DNA
Sample type SRA
 
Source name colon epthelial cells
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: wildtype
cell type: EDTA isolated colon epithelial cells
Treatment protocol mice were treated with 2% DSS for 3 day and isolated the colon epethelial cell
Growth protocol no treatment
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Sequence Analysis: The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.
Determination of Fragment Density: Since the 5´-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3´- ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 200 bp). To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined.
Peak Finding:The generic term “Interval” is used to describe genomic regions with local enrichments in tag numbers. Intervals are defined by the chromosome number and a start and end coordinate. MACS is used to identify the binding sites of transcription factors that bind to discrete sites.
Genome_build: mm10
Supplementary_files_format_and_content: bw
 
Submission date Mar 21, 2018
Last update date Mar 01, 2019
Contact name Yongfeng Liu
E-mail(s) lyf3433@163.com
Organization name The Institute of Health Sciences, SIBS, CAS / SJTUSM
Street address 320 Yueyang Road, Shanghai, 200025 P.R. China
City shanghai
ZIP/Postal code 200025
Country China
 
Platform ID GPL19057
Series (2)
GSE112127 Genome-wide assay of BRG1 regulated genes in inflamed colon epithelial cells
GSE112128 Function of BRG1 in colitis and colitis-associated-cancer
Relations
BioSample SAMN08765202
SRA SRX3826987

Supplementary file Size Download File type/resource
GSM3058263_2_00KJ_0027IHS_Colonic_epith_Input_mm10_i10_uniqnorm_signal.bw 163.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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