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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 08, 2017 |
| Title |
1-1-L-P1-M-Liver |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
age: P1
strain: C57BL/6
tissue: liver
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| Growth protocol |
Mice were maintained under standard conditions
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using a Qiagen all-prep DNA/RNA kit
RRBS libraries were constructed using the Truseq DNA LT kit, with a bisulfite treatment after adapter ligation. For locus specific bisulfite sequencing, we bisulfite treated DNA and PCR amplified regions of interest using primers with a 5' tail. A second PCR recognizing the 5' tail added barcode and adapter sequences.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Description |
Sequencing of specific loci after bisulfite conversion of genomic DNA
processed data file(s): LocusSpecificSummary.txt.gz
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| Data processing |
library strategy: locus specific bisulfite sequencing
We analyzed RRBS and locus specific bisulfite sequencing data by aligning fastq files to the mouse genome (mm9) using Bismark (v0.7.6) with bowtie2
We then combined replicates for each sample and summarized methylation data using the Bismark methylation_extractor.
We counted methylated and unmethylated CpGs at each genomic locus using perl scripts and imported the data into R for statistical analysis.
To remove uninformative CpG loci from RRBS data, we omitted any CpGs where greater than 10% of samples had coverage less than 10X. We then removed any CpGs that were unmethylated (<10%) in all samples of all ages. These CpGs are not informative for our study as they do not change between ages and introduce bias into the data because they are primarily located in CpG dense areas.
For locus specific data, we removed any data points with less than 100X coverage and any CpG where greater than 10% of samples had missing data.
Using R, we calculated the percent methylation at each locus for each sample and compared values between groups using a student’s t-test.
We derived false discovery rates (FDR) from t-test p-values using the qvalue package for R.
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: For RrbsSummary files, the columns are: chromosome, base, change in percent between ages, pvalue and qvalue. For LocusSpecificSummary.txt.gz, the columns are: locus chromosome, CpG identifier, age, sex, percentMethylation for that sample, pvalueOfChangeWithAge and qvalue
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| Submission date |
May 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Matt Cannon |
| E-mail(s) |
matthewvc1@gmail.com
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| Organization name |
Nationwide Children's Hospital
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| Department |
Center for Childhood Cancer
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| Street address |
700 Children's Dr.
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| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43205 |
| Country |
USA |
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| Platform ID |
GPL16417 |
| Series (1) |
| GSE58129 |
Postnatal Development is Associated with Genome-scale Changes in DNA methylation in Mouse Liver |
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| Relations |
| BioSample |
SAMN02808733 |
| SRA |
SRX556652 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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