|
| Status |
Public on Nov 10, 2012 |
| Title |
C INPUT vehicle donor5 |
| Sample type |
SRA |
| |
|
| Source name |
whole liver extract
|
| Organism |
Mus musculus |
| Characteristics |
age: 29-32 days
chip antibody: INPUT
treament: vehicle
tissue: liver
animal id: 5
experiment id: C
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 |
SRX192266 |
| BioSample |
SAMN01758913 |
