|
| Status |
Public on Aug 14, 2019 |
| Title |
RAd4_bulk_5 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cell
treatment: retinoic acid for 4 days
|
| Treatment protocol |
mESC were diffferentiated using "hanging drop" method. The formation of embryonic bodies were then grown in the well of a 6-well ultra-low attachment plate with differentiation medium containg 0.5 uM retinoic acid for up to 4 days, with the medium being changed daily.
|
| Growth protocol |
mESC were routingly grown in medium consisting of knockout DMEM supplemented with 15% knockout serum replacement with LIF growth factor. The cells were trypsinized when the cell density reached 80% confluent and replate on gelatin-coated plates.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with freshly prepared 1% formaldehyde and lysed with Hi-C lysis buffer.
For bulk HiChIP data, we followed the HiChIP protocol developed by Mumbach et al., using antibody to H3K27ac.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Retinoic-acid induction
|
| Data processing |
Library strategy: HiChIP
Reads are mapped to mm9 using HiC-Pro
Call loop by HiChIPPer
Genome_build: mm9
Supplementary_files_format_and_content: bedpe file contain all valid pairs
|
| |
|
| Submission date |
Mar 04, 2019 |
| Last update date |
Aug 17, 2019 |
| Contact name |
Zhana Duren |
| E-mail(s) |
durenzn@amss.ac.cn
|
| Organization name |
Stanford university
|
| Street address |
318 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
90304 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE127807 |
DC3: Deconvolution and coupled clustering from bulk and single cell genomics data |
|
| Relations |
| BioSample |
SAMN11051233 |
| SRA |
SRX5463272 |
