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Sample GSM1016432 Query DataSets for GSM1016432
Status Public on Nov 10, 2012
Title B H3K4me2 vehicle donor7
Sample type SRA
 
Source name whole liver extract
Organism Mus musculus
Characteristics age: 29-32 days
chip antibody: H3K4me2
treament: vehicle
tissue: liver
animal id: 7
experiment id: B
strain: B6C3F1/Crl (C57BL/6 male x C3H/He female)
Treatment protocol Phenobarbital (Sigma 04710, 0.05% (w/v) in drinking water) was administered to one group through ad libitum access to drinking water for 28 days
Growth protocol 29–32 days old male B6C3F1/Crl (C57BL/6 ♂ x C3H/He ♀) mice were obtained from Charles River Laboratories (Germany). Animals were allowed to acclimatise for 5 days prior to being randomly divided into two treatment groups of five animals each. Phenobarbital (Sigma 04710, 0.05% (w/v) in drinking water) was administered to one group through ad libitum access to drinking water for 28 days. Mice were checked daily for activity and behaviour and sacrificed on the last day of dosing (day 28)
Extracted molecule genomic DNA
Extraction protocol Extraction according to Thomson et al. Genome Biology 2012: Dynamic changes in liver 5‐ hydroxymethylcytosine profiles upon non‐ genotoxic carcinogen exposure
Library construction according to Thomson et al. Genome Biology 2012: Dynamic changes in liver 5‐ hydroxymethylcytosine profiles upon non‐ genotoxic carcinogen exposure
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Data processing base calling with CASAVA 1.8 for single-end and GERALD v1.52.6.1 for paired-end
for the paired-end data, mapping of reads with bowtie 0.12.7: bowtie --solexa1.3-quals -v 3 --best --strata -S -m 100 -5 11 -3 3 -I 0 -X 400
for the single-end data mapping was done with bowtie 0.12.5: bowtie --solexa1.3-quals -n 3 -l 36 --best --chunkmbs 512 --strata -S -m 100 -5 3
alignments were post-processed with samtools to create sorted and indexed BAM files
redundant alignments were removed (same alignment with same mismatches and genomic mapping)
the target genome was binned into 500 base pairs bins and reads counted per bin
the log2 fold change of IP (per sample and histone mark) over the input (background) is calculated
regions are further summarized (e.g. promotors, gene body), see supplementary file histoneMarkREsults3.txt
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files of enrichment (log2 library size normlaized read counts of IP over background) in bins of 500 base pairs; tab delimited enrichment (normalized by library size) of histone marks in different gene regions
 
Submission date Oct 05, 2012
Last update date May 15, 2019
Contact name John Paterson Thomson
E-mail(s) john.thomson@igmm.ed.ac.uk
Organization name University of Edinburgh
Department MRC Human Genetics Unit
Lab Meehan
Street address Crewe Road
City Edinburgh
ZIP/Postal code EH4 2XU
Country United Kingdom
 
Platform ID GPL11002
Series (2)
GSE40540 IP of 5-hydroxymethylcytosine (5-hmC) and 5-methylcytosine (5-mC) enriched DNA fragments from control and PB treated mouse livers
GSE41399 Changes in histone modifications H3K4me2, H3k27me3 and H3K36me3 due to phenobarbital in mice
Relations
SRA SRX192263
BioSample SAMN01758910

Supplementary file Size Download File type/resource
GSM1016432_100702_HWUSI-EAS1513_0006-s_6.bam.bedGraph.gz 29.6 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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