|
| Status |
Public on Oct 21, 2021 |
| Title |
PBMC_ASAP_Phage_compare_C_PDT |
| Sample type |
SRA |
| |
|
| Source name |
Peripherial Blood Mononucler Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Peripherial Blood Mononucler Cells
antigen capture: Phage nanobodies: anti-CD4, anti-CD8, anti-CD16, anti-CEACAM4
|
| 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_PDT_S4_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) |
[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 |
| GSE172923 |
Single-cell multi-modal profiling of proteins and chromatin accessibility using PHAGE-ATAC [ASAP_Phage_comparison] |
|
| Relations |
| BioSample |
SAMN18824581 |
| SRA |
SRX10654956 |
