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Sample GSM5259069 Query DataSets for GSM5259069
Status Public on Oct 21, 2021
Title PBMC_293T_Mix_ATAC
Sample type SRA
Source name Peripherial Blood Mononucler Cells and HEK293T cell line
Organism Homo sapiens
Characteristics cell mixing ratio: PBMCs and 293Ts at 2.5:1, 293Ts expressing either SARS-CoV-2 spike protein or EGFP
nb treatment: None
Treatment protocol Transfection using 4µg EGFP-GPI-encoding plasmid or 4µg SARS-CoV-2 spike protein encoding plasmid for HEK293T
Growth protocol Cryopreserved cells were thawed in DMEM with 10% FBS and washed in media. 293Ts were grown in DMEM + 10% FBS and 1x PenStrep
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_spike293_ATAC_S1_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.
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
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
GSE172920 Single-cell multi-modal profiling of proteins and chromatin accessibility using PHAGE-ATAC [Spike_mix_pbmcs]
BioSample SAMN18824591
SRA SRX10654952

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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