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Sample GSM4766872 Query DataSets for GSM4766872
Status Public on Oct 21, 2021
Title PBMC_Channel1_ATAC
Sample type SRA
 
Source name Peripherial Blood Mononucler Cells
Organism Homo sapiens
Characteristics cell type: Peripherial Blood Mononucler Cells
antigen capture: none
Treatment protocol NA
Growth protocol Cryopreserved cells were thawed in DMEM with 10% FBS and washed in media
Extracted molecule genomic DNA
Extraction protocol NP40 lysis, see method sections for full details
Custom 10x Genomics scATAC-seq
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Fastqs were generated using CellRanger-ATAC mkfastq v1.1.0
Sequencing reads were aligned using CellRanger-ATAC count for the hg38 reference genome
For Phage libraries, phage tag abundances were quantified per barcode using a custom unix script.
Genome_build: hg38
Supplementary_files_format_and_content: Per-barcode count abundance for phage library including the ATAC singlecell QC metrics; accessible chromatin fragments per atac library
 
Submission date Sep 04, 2020
Last update date Oct 21, 2021
Contact name Caleb Lareau
E-mail(s) lareauc@mskcc.org
Organization name Memorial Sloan Kettering
Street address 417 E 68th St, Zuckerman - ZRC 1132
City New York
State/province New York
ZIP/Postal code 10065
Country USA
 
Platform ID GPL18573
Series (2)
GSE157483 Single cell analysis of protein epitopes and chromatin accessibility using PHAGE-ATAC [Human_PBMCs]
GSE157486 Single cell analysis of protein epitopes and chromatin accessibility using PHAGE-ATAC
Relations
BioSample SAMN16058302
SRA SRX9075333

Supplementary file Size Download File type/resource
GSM4766872_PBMC_Channel1_ATAC_fragments.tsv.gz 859.3 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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