NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2840126 Query DataSets for GSM2840126
Status Public on Mar 08, 2018
Title sperm1B
Sample type SRA
 
Source name sperm
Organism Bos taurus
Characteristics tissue: sperm
breed: Holstein
developmental stage: adult
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 somatic tissues and 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 different lane for sperm1B 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), methylation level, coverage for methylated cytosine, coverage for unmethylated cytosine, total coverage
 
Submission date Nov 05, 2017
Last update date May 15, 2019
Contact name Yang Zhou
E-mail(s) yangzhou@mail.hzau.edu.cn
Phone 18162530091
Organization name Huazhong Agricultural University
Department College of animal science
Street address Shizishanjie #1
City Wuhan
State/province Hubei
ZIP/Postal code 430070
Country China
 
Platform ID GPL24230
Series (1)
GSE106538 Genome-wide sequencing and comparative profiling of cattle sperm DNA methylome
Relations
BioSample SAMN07982132
SRA SRX3367850

Supplementary file Size Download File type/resource
GSM2840126_sperm1B.bed.gz 293.8 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap