|
| 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) |
[email protected]
|
| 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 |
