|
| Status |
Public on Apr 20, 2018 |
| Title |
scATAC-seq_RA_D4_S64 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
cell line: R1
cell type: ESC
agent: RA
time: day 4
protocol: Retinoic-acid induction
|
| Treatment protocol |
EBs were placed in the well of a 6-well ultra-low attachment plate with fresh differentiation medium containing 0.5 mM retinoic acid (RA) for 4 days, with the medium being changed daily.
|
| Growth protocol |
mESC cells R1 were grown in mESC medium supplemented with 15% Knockout Serum Replacement and 1,000 U/ml of LIF. mESCs were differentiated using the handing drop method for 48 hours. Then, embryoid bodies (EBs) were collected for further treatment.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Single cells were captured and transposed with Tn5 using C1 fluidigm
scATAC-seq library were constructed by additional 13 cycles of PCR with dual index primers, followed by MinElute PCR purification.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads are mapped to mm9 using the ATAC-seq pipeline described in https://github.com/kundajelab/atac_dnase_pipelines.
We used MACS2 to perfom peak calling on aligned sequencing reads aggregated across all cells.
Genome_build: mm9
Supplementary_files_format_and_content: xlsx file showing read counts across peaks and cells
|
| |
|
| Submission date |
Dec 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Mahdi Zamanighomi |
| E-mail(s) |
[email protected]
|
| Organization name |
Stanford University
|
| Department |
Statistics
|
| Street address |
390 Serra Mall
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE107651 |
Unsupervised clustering and epigenetic classification of single cells |
|
| Relations |
| BioSample |
SAMN08128208 |
| SRA |
SRX3441672 |
