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Sample GSM3362518 Query DataSets for GSM3362518
Status Public on Mar 20, 2019
Title spermL01
Sample type SRA
 
Source name sperm
Organism Bos taurus
Characteristics tissue: sperm
breed: Holstein
developmental stage: adult
sire conception rate (scr): low
gestation length (gl): low
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.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model HiSeq X Ten
 
Description low_SCR;low_GL
different lane for spermL01 whole genome bisufite sequencing
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 (%)
 
Submission date Aug 30, 2018
Last update date Mar 20, 2019
Contact name Lingzhao Fang
E-mail(s) lingzhaofang@gmail.com
Organization name USDA
Department ARS
Lab Animal Genomics and Improvement Laboratory
Street address 10300 Baltimore Avenue
City Beltsville
State/province MD
ZIP/Postal code 20705
Country USA
 
Platform ID GPL24230
Series (1)
GSE119263 Comparative sperm methylome analysis provide insights into complex phenotypes and epigenome evolution
Relations
BioSample SAMN09938020
SRA SRX4626057

Supplementary file Size Download File type/resource
GSM3362518_L01.bed.gz 83.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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