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Sample GSM1020009 Query DataSets for GSM1020009
Status Public on Aug 09, 2013
Title Smc3 Wapl -/delta rep2
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 9148
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 [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
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
SRA SRX195362
BioSample SAMN01765670

Supplementary file Size Download File type/resource
GSM1020009_627BKAAXX_1_20110404a_9148_20110412_bowtie.bed.gz 57.8 Mb (ftp)(http) BED
GSM1020009_9148.peaks.txt.gz 405.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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