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| Status |
Public on Aug 14, 2017 |
| Title |
Dnmt3c rahu/rahu mouse u |
| Sample type |
SRA |
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| Source name |
whole testis
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| Organism |
Mus musculus |
| Characteristics |
tissue: whole testis
genotype: Dnmt3c rahu/rahu
strain: C57BL/6J & FVB/NJ (mixed); derived from ENU mutagenized line
age: 12 days post partum
littermate: litter 2
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| 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.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
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| 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 %).
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| Submission date |
Jul 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Cem Meydan |
| Organization name |
Weill Cornell Medical College
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| Department |
Physiology & Biophysics
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| Lab |
Melnick Lab & Mason Lab
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| Street address |
1305 York
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN07336328 |
| SRA |
SRX2991440 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2698075_MUT242_CpG.methylKit.txt.gz |
332.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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