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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 04, 2024 |
| Title |
F1 ram sperm, CON, rep4 |
| Sample type |
SRA |
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| Source name |
semen
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| Organism |
Ovis aries |
| Characteristics |
tissue: semen
cell line: sperm
cell type: sperm
genotype: WT
treatment: Standard feeding
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
the sperm were treated with somatic cell lysis buffer (0.1 % SDS, 0.5 % Triton X in DEPC H2O) for 40 min on ice to eliminate somatic cell contamination, followed by centrifugation at 600g for 5 minutes. The sperm pellet was washed and used for DNA extraction using TRIzol reagent.
DNA extraction, MspI digestion, end-repair, dA-tailing, adaptor ligation, and bisulfite conversion were conducted in a single tube to minimize DNA loss. Amplified DNA fragments of 200 to 500 bp were size selected using a 2% agarose gel.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The sequencing adapters were removed by TrimGalore-0.4.3
The reads were removed if they had a quality score lower than 20, length less than 36 and a total number of 15 Ns or more. FastQC
The first 12 bp at the 5′ end of both pairs were found to be of low quality and removed. Trimmed sequences were mapped to the bovine genome UMD3.1.1 using Bismark - v.0.18.1
Assembly: Oar_v4.0/oviAri4
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| Submission date |
Feb 23, 2023 |
| Last update date |
Apr 04, 2024 |
| Contact name |
Zongliang Jiang |
| Organization name |
University of Florida
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| Department |
Animal Sciences
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| Street address |
2033 Mowry Rd
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| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32610 |
| Country |
USA |
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| Platform ID |
GPL27721 |
| Series (2) |
| GSE225924 |
Maternal gestational nutrition perturbs offspring sperm epigenome in sheep [BiSulfite-seq] |
| GSE225988 |
Maternal gestational nutrition perturbs offspring sperm epigenome in sheep |
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| Relations |
| BioSample |
SAMN33424293 |
| SRA |
SRX19483480 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7060417_cnt96_CpG.txt.gz |
22.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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