|
| Status |
Public on Apr 24, 2024 |
| Title |
20pg rep2 |
| Sample type |
SRA |
| |
|
| Source name |
mouse ESCs
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
technology: ABS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified using Qiagen's Puregene kit and sonicated to about 200 bp.
Methylated adapters were added with the NEBNext DNA library prep kit. Libraries were bisulfite converted with the Zymo EZ DNA Methylation Lightning kit.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
Trimmed reads were mapped to mouse genome mm9 by bismark.
Only uniquely mapped reads were kept for down-stream analyses.
Calling of mC was performed by scripts in bismark.
Genome_build: mm9
Supplementary_files_format_and_content: bismark output cov files
|
| |
|
| Submission date |
Oct 15, 2021 |
| Last update date |
Apr 24, 2024 |
| Contact name |
Xiaolong Cui |
| E-mail(s) |
xiaolong.cui@northwestern.edu
|
| Organization name |
Northwestern University
|
| Department |
Department of Preventive Medicine
|
| Street address |
680 N Lake Shore Drive
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE186007 |
LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA |
|
| Relations |
| BioSample |
SAMN22329931 |
| SRA |
SRX12633807 |
