 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 08, 2018 |
| Title |
WBC3842 |
| Sample type |
SRA |
| |
|
| Source name |
blood
|
| Organism |
Bos taurus |
| Characteristics |
tissue: blood
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 WBC3842 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 |
SAMN07982136 |
| SRA |
SRX3367857 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2840133_WBC3842.bed.gz |
305.0 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
