|
| Status |
Public on Jun 13, 2021 |
| Title |
15-month KIT+ input |
| Sample type |
SRA |
| |
|
| Source name |
Spermatogonial progenitor cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6;CBA-Tg(Pou5f1-EGFP)2Mnn/J
cell source: Oct4-GFP+ germ cells
age: 15 months
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiments and ChIP-Seq libraries were prepared using Diagenode True MicroChIP kit according to the manufacturer's protocol. 0.2 million freshly sorted Oct4-GFP+/KIT- or Oct4-GFP+/KIT+ cells were cross-linked with 1% formaldehyde for 10 minutes. The crosslinking was stopped by incubation with 0.125M glycine at room temperature for 5 minutes. Chromatin was fragmented to 200 to 600 bp by sonication using a Bioruptor sonicator (Diagenode, Liège, Belgium). 1ug antibodies against H3K4me3 or H3K27me3 were used for ChIP. Half of the chromatin was used for each IP, and 10% of the chromatin solution was reserved as input control.
The chromatin immunoprecipitated (ChIPed) DNA was subjected to library preparation using MicroPlex Library Preparation kit (Diagenode, Liège, Belgium). The prepared library was sequenced with single-end 50bp reads using the Illumina HiSeq 2000.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
KIT+ cells from 15-month-old mice
|
| Data processing |
Reads were mapped to the mouse genome (mm9 assembly) using Bowtie (Langmead et al., 2009). Mapped reads were filtered for PCR duplicates using MACS2 (Zhang et al., 2008). Peak calling and visualization of tracks were done using EaSeq (Lerdrup et al., 2016).
none provided by the submitter
Genome_build: mm9
|
| |
|
| Submission date |
Jan 11, 2021 |
| Last update date |
Jun 13, 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) |
| GSE164603 |
Epigenetic profiling of young and aged spermatogonial stem cells (ChIP-Seq) |
| GSE164607 |
Transcriptomic and epigenomic profiling of young and aged spermatogonial stem cells reveals molecular targets regulating differentiation |
|
| Relations |
| BioSample |
SAMN17284693 |
| SRA |
SRX9823183 |
