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| Status |
Public on May 20, 2014 |
| Title |
livers group f |
| Sample type |
SRA |
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| Source name |
livers group f
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| Organism |
Rattus norvegicus |
| Characteristics |
diet: low protein+folate
strain: Wistar
gender: male
age: 1 day
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was isolated and fragmented by sonication; MBD fusion protein was incubated with fragmented DNA.
Genomic DNA from rat livers was subjected to selection according to the methyl-CpG binding domain-based (MBD) protein protocol (DNA pooled from 6 individuals per group) and the resulting fragments sequenced in high throughput. Methylated DNA was captured with MethylCap kit (Diagenode). Approximately 10 ng of captured DNA was used for library preparation (ChIP-seq DNA sample Prep Kit, Illumina).
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| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
dna methylation profile from livers of 6 animals in group f
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| Data processing |
base calling was performed by the genomic facility, presumably using CASAVA
1st: normalization using Medips, rpm, , R-Bioconductor package
1st bis: quality control using fastq, inhouse software and genome browser
2nd: alignment to the genome using Bowtie
2nd bis: quality control (aligned reads count,visualization)
3rd: peak calling using MACS
4th: genomic annotation (ENSEMBL API,GREAT)
5th: biological annotation (GSEA,GREAT)
Genome_build: rn4
Supplementary_files_format_and_content: wig, normalized methylation profiles (step 1)
Supplementary_files_format_and_content: peaks.bed: peak calling using MACS
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| Submission date |
Sep 17, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Gioia Altobelli |
| E-mail(s) |
[email protected]
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| Organization name |
UCL
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| Street address |
5 University Street
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| City |
London |
| ZIP/Postal code |
WC1E 6JF |
| Country |
United Kingdom |
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| Platform ID |
GPL10287 |
| Series (1) |
| GSE50935 |
Genome wide effects of maternal undernutrition |
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| Relations |
| BioSample |
SAMN02358167 |
| SRA |
SRX352165 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1232712_folate.mbd-balign-rpm.WIG.gz |
14.1 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data are available in SRA |
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