|
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 |
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 |
GSE172920 |
Single-cell multi-modal profiling of proteins and chromatin accessibility using PHAGE-ATAC [Spike_mix_pbmcs] |
|
Relations |
BioSample |
SAMN18824591 |
SRA |
SRX10654952 |