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Sample GSM1020006 Query DataSets for GSM1020006
Status Public on Aug 09, 2013
Title Smc3 Wapl +/delta rep1
Sample type SRA
 
Source name mouse embryonic fibroblasts
Organism Mus musculus
Characteristics cell type: embryonic fibroblast
genotype: Wapl +/delta
genetic background: mixed C57BL/6 and 129 background
chip antibody: rabbit anti-Smc3
chip antibody manufacturer: Bethyl
chip antibody catalog #: A300-060A
Treatment protocol 4-OHT was added to the starvation medium to a final concentration of 500 nM
Growth protocol MEFs were starved in OptMEM containing 2% serum for seven days
Extracted molecule genomic DNA
Extraction protocol Samples were sonicated for 12 x 60 second pulses with a Covaris sonicator; DNA was purified with Phase lock gel tubes (5PRIME)
Single read - Illumina
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description 8740
Data processing Alignment: Reads that passed the Illumina quality filtering were considered for alignment. The remaining reads were aligned against the mouse genome assembly version July 2007 (NCBI37/mm9) using the BOWTIE program version 12.5 [Langmead, 2009], allowing up to two mismatches, and ignoring any read that would match more than once.
Peak calling: Peaks were called using the MACS program version 1.3.6.1 [Zhang et al.] with default parameters and appropriate tag size, mm9 genome size (2654911517), sample and input read files. In cases where the read shifting model could not be build with the default mfold parameter (32), the mfold cutoff was lowered up to the point where sufficient high quality peaks could be found to build the model (100). Peaks were further filtered for p-values lower than 1e-10. This cutoff is more conservative than the default (1e-5), and worked well in removing false positive (=unique) peaks of technical replicates [data not shown].
Genome_build: mm9
Supplementary_files_format_and_content: BED files contain all uniquely aligned reads or called peaks
 
Submission date Oct 15, 2012
Last update date May 15, 2019
Contact name Roman R Stocsits
E-mail(s) roman.stocsits@imp.ac.at
Organization name IMP - Research Institute of Molecular Pathology
Lab Jan-Michael Peters' Lab
Street address Campus-Vienna-Biocenter 1
City Vienna
ZIP/Postal code 1030
Country Austria
 
Platform ID GPL11002
Series (2)
GSE41602 Wapl controls higher-order chromatin structure in interphase chromosomes (ChIP-Seq)
GSE41603 Wapl controls higher-order chromatin structure in interphase chromosomes
Relations
SRA SRX195359
BioSample SAMN01765667

Supplementary file Size Download File type/resource
GSM1020006_6220CAAXX_7_20100802a_8740_20100803_bowtie.bed.gz 74.8 Mb (ftp)(http) BED
GSM1020006_8740.peaks.txt.gz 840.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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