|
| Status |
Public on Jul 17, 2020 |
| Title |
Kit_bisulfite-seq |
| Sample type |
SRA |
| |
|
| Source name |
testis
|
| Organism |
Mus musculus |
| Characteristics |
tissue: testis
cell type: differentiated spermatogonia cells
development stage: 6-8 days post-natal
strain: C57BL/6
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA is extracted through Wizard Genomic DNA Purification Kit（LOT 0000139127）.
The sequencing libraries were generated using the Pico Methyl-Seq Library Prep Kit (D5456, Zymo Research) following the manufacturer's instructions.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
whole genome
marker: kit
KIT-antibody manufacturer : Biolegend lot number:B255217
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using using bsmap(v 2.89) with parameter “--s 16 -v 0.1 -n 1 -R".
Methylation level of each CpG site was estimated using mcall(v 1.3.0) with default parameters, and output bed format files are transformed to tab-delimited text files using custom python scripts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include methylation level and coverage for each CpG site.
|
| |
|
| Submission date |
Sep 19, 2019 |
| Last update date |
Jul 18, 2020 |
| Contact name |
liu ying dong |
| E-mail(s) |
liuyingdong2017@126.com
|
| Phone |
18729187605
|
| Organization name |
Northwest University of Agriculture and Forestry Science and Technology
|
| Department |
College of Animal Science and Technology
|
| Lab |
Zeng wenxian
|
| Street address |
Shaanxi
|
| City |
Xi'an, Shaanxi |
| ZIP/Postal code |
710000 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE137743 |
Whole genome bisulfite Sequencing data of four types mouse spermatogenesis |
| GSE137744 |
ltra-low-input native ChIP-seq and Whole genome bisulfite Sequencing data of four types mouse spermatogenesis |
|
| Relations |
| BioSample |
SAMN12788971 |
| SRA |
SRX6874359 |
