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| Status |
Public on Mar 20, 2019 |
| Title |
spermL09 |
| Sample type |
SRA |
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| Source name |
sperm
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| Organism |
Bos taurus |
| Characteristics |
tissue: sperm
breed: Holstein
developmental stage: adult
sire calving ease (sce): low
cow conception rate (ccr): low
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA).
The qualified genomic DNA from sperm were used to construct libraries. Briefly, 3 μg of genomic DNA spiked with unmethylated lambda DNA were fragmented into 200-300 bp using a Covaris S220 (Covaris, Inc., Woburn, MA, USA), followed by teriminal repairing and A-ligation. Different cytosine methylated barcodes were ligated to sonicated DNA for different samples. The DNA bisufite conversion was performed using the EZ DNA Methylation Gold Kit (Zymo Research, Irvine, CA, USA). Then single-stranded DNA fragments were amplified using the KAPA HiFi HotStart Uracil + ReadyMix (2 X) (Kapa Biosystems, Wilmington, MA, USA). The library concentration was quantified using a Qubit 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA) and qPCR (iCycler, BioRad Laboratories, Hercules, CA, USA), and the insert size was checked using the Agilent 2100.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
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| Description |
low_SCE;low_CCR
different lane for spermL09 whole genome bisufite sequencing
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| Data processing |
Programs FastQC (0.11.2) and Trim Galore (0.4.0) were used to generate sequence quality reports and to trim/filter the sequences, respectively.
The cleaned data for each sample were merged and aligned to the reference genome (Bos taurus UMD3.1) using bowtie2 under the Bismark software (0.14.5)
The methylcytosine information was extracted using the bismark_methylation_extractor after deduplicating the duplication reads.
Genome_build: UMD3.1
Supplementary_files_format_and_content: The data files contain the methylatin information for the CG detected. The column names are: chrmosome, position, position (same as the second column), total coverage, methylation level (%) for cytosine, unmethylated cytosine (%)
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| Submission date |
Aug 30, 2018 |
| Last update date |
Mar 20, 2019 |
| Contact name |
Lingzhao Fang |
| E-mail(s) |
lingzhaofang@gmail.com
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| Organization name |
USDA
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| Department |
ARS
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| Lab |
Animal Genomics and Improvement Laboratory
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| Street address |
10300 Baltimore Avenue
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| City |
Beltsville |
| State/province |
MD |
| ZIP/Postal code |
20705 |
| Country |
USA |
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| Platform ID |
GPL24230 |
| Series (1) |
| GSE119263 |
Comparative sperm methylome analysis provide insights into complex phenotypes and epigenome evolution |
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| Relations |
| BioSample |
SAMN09938012 |
| SRA |
SRX4626065 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3362526_L09.bed.gz |
35.4 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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