|
Status |
Public on Apr 20, 2018 |
Title |
scATAC-seq_RA_D4_S95 |
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 |
SAMN08128276 |
SRA |
SRX3441703 |