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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 17, 2015 |
| Title |
C2 |
| Sample type |
SRA |
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| Source name |
Spermatozoa_WGBS_10weeks_control
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| Organism |
Mus musculus |
| Characteristics |
age: 10 weeks
strain: C57BL/6; FVB/NJ
tissue: Cauda epididymis and vas deferens
cell type: Spermatozoa
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| Treatment protocol |
Sibling male mice were split at weaning (3 weeks) onto control or low protein, or control or high fat diets. Mice were maintained on these diets until sacrifice at 10 weeks.
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| Growth protocol |
Sibling male mice were split at weaning (3 weeks) onto control or low protein, or control or high fat diets. Mice were maintained on these diets until sacrifice at 10 weeks.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cauda epididymis and vas deferens was rapidly dissected and punctured, and was incubated in 500 ¼L of human tubule fluid (HTF - Millipore MR-070-D) at 37 C for 30 minutes. Supernatant was removed, sperm were pelleted at 2000 g for 5 minutes, washed once with 1 mL water and then pelleted. Sperm were washed again with 1 mL PBS, and pelleted again. Sperm were resuspended in 400 ¼L DNA Lysis Buffer (10mM Tris, 5mM EDTA, 0.5% SDS, and 200mM NaCl) with 10mM DTT, and incubated at 37oC for 30 minutes. Sperm were subjected to needle homogenization. 20 ¼g/mL Proteinase K was added to the homogenate and incubated at 55oC for 16 hours. DNA was extracted with Phenol:Chloroform:Isoamyl Alcohol and precipitated with 100% EtOH.
DNA was sheared to an average length of ~100-500 bp with a Covaris sonicator, fragment ends were cleaned up and A-tailed. Fragments were ligated to pre-methylated Illumina paired-end adaptors, bisulfite converted, and PCR-amplified.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
WGBS
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| Data processing |
bsmap, v2.73, default
Genome_build: Illumina NextSeq:mm10, Illumina HiSeq 2500: mm9
Supplementary_files_format_and_content: Methylation calls could not be located. Processed data are not available for this study.
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| Submission date |
Dec 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Alper Kucukural |
| E-mail(s) |
alper.kucukural@umassmed.edu
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| Phone |
7743124493
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| Organization name |
UMass Medical School
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| Department |
Program in Molecular Medicine
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| Lab |
Biocore
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| Street address |
364 Plantation Street
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| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE75323 |
Genetic and Epigenetic Variation, but Not Diet, Shape the Sperm Methylome |
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| Relations |
| BioSample |
SAMN04346873 |
| SRA |
SRX1485696 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not provided for this record |
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