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Sample GSM1174211 Query DataSets for GSM1174211
Status Public on Oct 01, 2015
Title Tumors PBS Control (MACS)
Sample type SRA
 
Source name Pooled gastric tumor tissue from 3 individual PBS-treated gp130F/F mice, Stat3 ChIP
Organism Mus musculus
Characteristics genotype/variation: gp130F/F
tissue: gastric tumors
age: 10-12 weeks
treatment: PBS
chip antibody: anti-Stat3
Treatment protocol Mice (10-12 weeks, n=3 per treatment cohort) were subjected to a single intraperitoneal injection of PBS (200ul), IL6 or IL11 (5ug diluted in 200ul PBS) 60 min prior to sacrifice. Gastric tumor tissue was resected, snap-frozen on dry ice and stored at -80 degrees Celsius.
Extracted molecule genomic DNA
Extraction protocol Following DNA-Protein cross-linking with formaldehyde and tissue homogenization, chromatin was extracted using "shearing buffer" provided in the SIGMA Imprint ChIP Kit in accordance with the manufacturer's instructions. Chromatin shearing was performed using the Diagenode Bioruptor water bath sonicator. Sheared chromatin was used for immunoprecipitations with a ChIP-validated Stat3 antibody (Santa Cruz SC-482X) and the SIGMA Imprint ChIP Kit according to the manufacturer's instructions.
Libraries were prepared according to Illumina's instructions accompanying the ChIP-Seq DNA Sample Preparation Kit (IP-102-1001). 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 Exo fragment 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. Following adapter ligation, DNA was PCR amplified (15 cycles) with Illumina primers, and library fragments of 200-300 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 II following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description Control
Chromatin
Data processing Base-calling: Base-calling was performed using Illumina software. Reads that have poor sequence quality and/or are made of homopolymers were removed from the datasets.
Read alignment: After filtering of poor quality sequences, ChIP-Seq reads were aligned to the UCSC mm9 genome assembly using Bowtie software.
File conversion: Conversion of Bowtie output files to .bed and .wig files was performed using Perl.
Peak calling: Peak calling was performed using MACS software (Zheng et al., 2008) with a fold-enrichment ratio (mfold) of 12 fold and a standard threshold probability (p-value) of P≤10-5.
Retrieval of relevant peak and associated gene/microRNA information was performed using R programming language for statistical computing (Version 2.12.1).
Genome_build: MGSCv37
Supplementary_files_format_and_content: .bed and .xls files. The three processed data files "Control_Peak_Information_MACS_Output.xls", "IL6_Peak_Information_MACS_Output.xls" and "IL11_Peak_Information _MACS_Output.xls" are the original output files of the MACS software and contain the following information about significant Stat3-associated peaks: (I) exact peak location (chromosome number and the start and end nucleotide positions), (II) peak width/length (expressed in base pairs), (III) peak summit (the exact nucleotide position in each peak at which the highest number of tags were counted), (IV) reads/tags per peak (total number of sequence tags counted at each enriched region ), (V) P-value and (VI) fold enrichment of each peak.
 
Submission date Jun 25, 2013
Last update date May 15, 2019
Contact name Stefan Thiem
E-mail(s) SteThiem@gmail.com
Phone +61-3-9496-9775
Organization name Olivia Newton-John Cancer Research Institute
Department Cancer Research
Lab Cancer & Inflammation Laboratory
Street address 145 Studley Road
City Heidelberg - Melbourne
State/province Victoria
ZIP/Postal code 3084
Country Australia
 
Platform ID GPL9250
Series (2)
GSE48285 Genome-wide ChIP-Seq analysis of genomic Stat3 binding sites in murine gastric tumors following stimulation with IL6 or IL11 (MACS)
GSE48288 Genome-wide ChIP-Seq analysis of genomic Stat3 binding sites in murine gastric tumors following stimulation with IL6 or IL11
Relations
Reanalyzed by GSM1174238
BioSample SAMN02213663
SRA SRX315094

Supplementary file Size Download File type/resource
GSM1174211_Control_MACS_Peaks.bed.gz 4.5 Kb (ftp)(http) BED
GSM1174211_Control_Peak_Information_MACS_Output_.xls.gz 23.4 Kb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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