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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 20, 2014 |
| Title |
26sr2 |
| Sample type |
SRA |
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| Source name |
DNA from striatum brain tissue
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| Organism |
Mus musculus |
| Characteristics |
tissue: brain
brain region: striatum
strain: DBA2/J
methylation enrichmant kit: MethylMiner
elution buffer salt concentration: Low salt
elution approach: NA
double barcodes: NA
duplicate number: 2
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Gentra Puregene Blood/Tissue Kit (Qiagen, Valencia, CA) following the vendor’s instructions. The DNA was fragmented into a median length of 180 base pairs using ultrasonication with the Covaris S2 instrument (Covaris, Woburn, MA, USA). The amount of starting material for each methylation enrichment reaction was 1.5 µg of DNA for both MethylMiner and MethylCap.
The methylation-enriched DNA from MethylMiner and MethylCap, respectively, was used as input materials for barcoded fragment libraries for SOLiD5500xl Wildfire deep sequencing. Each library was sequenced using single-end chemistry at 50 bp read length.
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| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
AB 5500xl-W Genetic Analysis System |
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| Description |
For each of the 19 autosomal chromosomes the described files are available for each sample in a tar archive.
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| Data processing |
The sequenced reads were aligned using BioScope 1.2 (Life Technologies)
We followed a previously developed an analysis pipeline for MBD-seq that includes rigorous quality control for methylome-wide investigations. Aberg KA, McClay JL, Nerella S, Xie LY, Clark SL, et al. (2012) MBD-seq as a cost-effective approach for methylome-wide association studies: demonstration in 1500 case-control samples. Epigenomics 4: 605-621.
Coverage estimates were generated using a previusly described approach.van den Oord EJ, Bukszar J, Rudolf G, Nerella S, McClay JL, et al. (2013) Estimation of CpG coverage in whole methylome next-generation sequencing studies. BMC Bioinformatics 14: 50.
Genome_build: Mouse samples were aligned to the DBA2/J (D2) specific reference genome. Wang X, Agarwala R, Capra JA, Chen Z, Church DM, et al. (2010) High-throughtput sequenceing of the DBA/2J mouse genome. BMC Bioinformatics 11(Suppl 04): O7.
Supplementary_files_format_and_content: CpG-coverage file provided in comma delimited files (.csv), for each CpG coordinate in the reference genome the estimated coverage is given, which is a measure of the methylation status of that specific location ; nonCpG-coverage file provided in comma delimited files (.csv), for each nonCpG coordinate ( a C that is at least 400 bp away from any CpG coordinate) in the reference genome the estimated coverage is given, which is a measure of the background noise of that specific location.
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| Submission date |
Dec 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Karolina A Aberg |
| Organization name |
Virginia Commonwealth University
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| Department |
Center for Biomarker Resarch & Personalized Medicine
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| Street address |
1112 East Clay Street
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| City |
Richmond |
| State/province |
VA |
| ZIP/Postal code |
23298 |
| Country |
USA |
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| Platform ID |
GPL18061 |
| Series (1) |
| GSE64144 |
Evaluation of methyl-binding domain based enrichment approaches revisited |
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| Relations |
| BioSample |
SAMN03264785 |
| SRA |
SRX808123 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1565263_26sr2.all.CpG_coord.csv.tar.gz |
163.2 Mb |
(ftp)(http) |
TAR |
| GSM1565263_26sr2.all.nonCpG_coord.csv.tar.gz |
1.2 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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