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Sample GSM2875171 Query DataSets for GSM2875171
Status Public on Apr 20, 2018
Title scATAC-seq_RA_D4_S47
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 SAMN08127981
SRA SRX3441655

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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