|
| Status |
Public on Jun 13, 2021 |
| Title |
6-8-month KIT- oxRRBS rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Spermatogonial stem cell (SSC)
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6;CBA-Tg(Pou5f1-EGFP)2Mnn/J
cell source: Oct4-GFP+ germ cells
age: 6-8 months
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
1 million primary cells of each population in two independent experiments were FACS-sorted as described above. Genomic DNA was isolated from each cell fraction using the AllPrep DNA/RNA Mini kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions.
0.5ug of genomic DNA was digested with MspI followed by end repair, A-tailing, and ligation of adaptors. Adaptor-ligated MspI-digested DNA was size-selected (110-380 bp) and purified. 1/5 the DNA was kept for the generation of the non-oxidized library and remaining DNA was subjected to oxidation. Both oxidized and non-oxidized DNA samples were bisulfite-treated. Final library amplification was carried out for 18 cycles, after which the libraries were purified using AMPure XP beads (Agencourt) and sequenced on Illumina platform.
1 million primary cells of each population in two independent experiments were FACS-sorted as described above. Genomic DNA was isolated from each cell fraction using the AllPrep DNA/RNA Mini kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions.
0.5ug of genomic DNA was digested with MspI followed by end repair, A-tailing, and ligation of adaptors. Adaptor-ligated MspI-digested DNA was size-selected (110-380 bp) and purified. 1/5 the DNA was kept for the generation of the non-oxidized library and remaining DNA was subjected to oxidation. Both oxidized and non-oxidized DNA samples were bisulfite-treated. Final library amplification was carried out for 18 cycles, after which the libraries were purified using AMPure XP beads (Agencourt) and sequenced on Illumina platform.
RRBS and oxRRBS.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
KIT- cells from 6 to 8-month-old mice
|
| Data processing |
The raw reads were quality-checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and low-quality reads and adapters were removed using Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using '--rrbs' trimming mode. Trimmed sequences were mapped to the mouse genome with Bismark (Krueger and Andrews, 2011).
Genome_build: mm9
|
| |
|
| Submission date |
Jan 11, 2021 |
| Last update date |
Jun 14, 2021 |
| Contact name |
Jinyue Liao |
| E-mail(s) |
liaojinyue@cuhk.edu.hk
|
| Organization name |
The Chinese University of Hong Kong
|
| Department |
Department of Chemical Pathology
|
| Street address |
Room 38016, 1/F Lui Che Woo Clinical Sciences Building
|
| City |
Hong Kong |
| ZIP/Postal code |
000000 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE164606 |
Epigenetic profiling of young and aged spermatogonial stem cells (RRBS) |
| GSE164607 |
Transcriptomic and epigenomic profiling of young and aged spermatogonial stem cells reveals molecular targets regulating differentiation |
|
| Relations |
| BioSample |
SAMN17284754 |
| SRA |
SRX9823211 |
