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Sample GSM917531 Query DataSets for GSM917531
Status Public on Jan 01, 2013
Title Pol2_KO_CT6_ChIPSeq
Sample type SRA
 
Source name Mll3∆/∆ MEF
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Mll3∆/∆ MEF
chip antibody: Pol2
antibody vendor: Abcam
antibody cat#: ab817
time point: CT6
Extracted molecule genomic DNA
Extraction protocol Chromatin was sheared using a Diagenode Bioruptor at 4oC, using conditions optimised to produce 150-300bp fragments with the use of 15 ml Falcon tubes holding 2ml of lysate each (30 cycles of 30 secs on HIGH, 30 secs OFF). Sheared chromatin was transferred to 1.5 ml microcentrifuge tubes and spun at 14,000 rpm for 15 min at 4°C to pellet debris. Cleared supernatants were transferred to clean microcentrifuge tubes and 100 µl from each sample lysate was saved for use as an input control for sequencing and to check fragment size distribution. standard Illumina indexing primers were used, as per the manufacturer’s instructions. All libraries were multiplexed, and 4 indexed pooled samples (corresponding to four time-points, CT0, 6, 12, 18) sequenced per lane.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description Chromatin IP against Pol2
Data processing Raw paired-end 50bp reads (in FASTQ format) were aligned to the UCSC mm9 genome build with Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) using pre-built indexes downloaded from the host website. Parameters were optimised to utilise the software’s multi-threading capabilities (we typically used a 128-core cluster for alignments). Alignment files were then converted from the standard Bowtie output format to ALN files (for use with Cisgenome) using a custom Perl script. Alignments were then analysed using a 2-sample comparison (ChIPed sample vs. Input control for each time-point) with Cisgenome v1, using a cut-off false discovery rate of 10% and a sliding window size of 100. Output files were converted into various formats for browsing datasets and to display data. The Cisgenome and UCSC browsers were used for data visualisation, using custom tracks
 
Submission date Apr 18, 2012
Last update date May 15, 2019
Contact name Utham Kashyap Valekunja
Organization name University of Pennsylvania
Department Department of Systems Pharmacology & Therapeutics, Perelman School of Medicine,
Lab 10-179/180 Smilow Center for Translational Research,
Street address 3400 Civic Center Boulevard,
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL11002
Series (2)
GSE37393 Daily cycling of genome-wide histone methylation
GSE37396 The histone methyltransferase MLL3 regulates genome-scale circadian transcription
Relations
SRA SRX143293
BioSample SAMN00858145

Supplementary file Size Download File type/resource
GSM917531_Pol2_KO_CT6.bar.txt.gz 212.1 Kb (ftp)(http) TXT
GSM917531_Pol2_KO_CT6_aligned.txt.gz 377.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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