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Sample GSM5259079 Query DataSets for GSM5259079
Status Public on Oct 21, 2021
Title PBMC_ASAP_Phage_compare_C_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 NextSeq 550
 
Description combEF_PBMC_C_ATAC_S3_L001
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.
For ASAP libraries, 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 Apr 21, 2021
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 GPL21697
Series (2)
GSE157486 Single cell analysis of protein epitopes and chromatin accessibility using PHAGE-ATAC
GSE172923 Single-cell multi-modal profiling of proteins and chromatin accessibility using PHAGE-ATAC [ASAP_Phage_comparison]
Relations
BioSample SAMN18824582
SRA SRX10654955

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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