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Sample GSM2698072 Query DataSets for GSM2698072
Status Public on Aug 14, 2017
Title Dnmt3c+/+ mouse v′
Sample type SRA
Source name whole testis
Organism Mus musculus
Characteristics tissue: whole testis
genotype: Dnmt3c +/+
strain: C57BL/6J & FVB/NJ (mixed); derived from ENU mutagenized line
age: 12 days post partum
littermate: litter 2
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from whole testis by incubating a single testis in 200 μl of DirectPCR lysis reagent (Viagen) containing 1 μl of proteinase K solution (>600 mAU/ml, Qiagen) for 24 hr at 55°. DNA was subsequently RNase A-treated, phenol:chloroform-extracted, and ethanol-precipitated.
Whole-genome bisulfite libraries were prepared and sequenced at the New York Genome Center (NYGC) using a tagmentation-based protocol developed by NYGC and J. Greally. In brief, 100 ng of genomic DNA was fragmented using tagmentation by Tn5 transposase and purified by Silane bead cleanup (Dynabeads MyOne Silane, Thermo Fisher Scientific). End filling was performed using dATP, dGTP, dTTP and methylated dCTP to protect added cytosines from bisulfite treatment. End-repaired DNA was purified by SPRI bead cleanup (Beckman), and subjected to bisulfite treatment and cleanup using EZ DNA Methylation-Gold MagPrep kit (Zymo Research). Illumina sequencing adapters (standard i5 adapter and custom i7 adapter) were added using PCR amplification. Finally, size selection of 300-bp to 800-bp fragments was performed using SPRI bead cleanup (Beckman). Libraries were sequenced with standard Illumina read 1 primer and custom read 2 and i7 index primers. Control library generated from Kineococcus radiotolerans was spiked at 20% to enhance library complexity.
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model HiSeq X Ten
Data processing Adapter sequence were first N-masked from raw FASTQ files using cutadapt v1.9.1.
Short-read alignment was performed with bwa-meth. We modified bwa-meth’s default minimum longest match length for a read (0.44*read-length) to greater than 30 bp (0.2*read-length).
The resulting alignment files were marked for duplicates using Picard v2.4.1.
Methylation levels were calculated using MethylDackel v0.1.13 at cytosines excluding quality control failed, supplemental, duplicate, and MAPQ less than 20 reads (which excluded multi-mapped reads). Additionally, bases with quality less than 20 or within the first 11 bases sequenced on either read pair were also excluded.
Genome_build: mm10 (NCBIM38)
Supplementary_files_format_and_content: text file with methyl call. Headers are: 1. position id (chr.base), 2. chr, 3. position, 4. strand, 5. coverage, 6. C% in bisulfite-seq (methylated read %), 7. T% in bisulfite-seq (unmethylated read %).
Submission date Jul 08, 2017
Last update date May 15, 2019
Contact name Cem Meydan
Organization name Weill Cornell Medical College
Department Physiology & Biophysics
Lab Melnick Lab & Mason Lab
Street address 1305 York
City New York
State/province New York
ZIP/Postal code 10065
Country USA
Platform ID GPL21273
Series (2)
GSE100959 rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline [WGBS]
GSE100960 rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline
BioSample SAMN07336331
SRA SRX2991437

Supplementary file Size Download File type/resource
GSM2698072_WT240_CpG.methylKit.txt.gz 334.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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