|
| Status |
Public on Oct 21, 2021 |
| Title |
SpeciesMix_eGFP_Known_Phage |
| Sample type |
SRA |
| |
|
| Source name |
Cell line
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell mixture: 25% eGFP+ HEK293T; 25% eGFP- HEK293T; 50% NIH3T3
ab treatment: Known GFP
|
| Treatment protocol |
Transfection using 4µg EGFP-GPI-encoding plasmid for HEK293T
|
| Growth protocol |
DMEM, 10%FBS, Pen/Strep
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
NP40 lysis, see method sections for full details
Custom 10x Genomics scATAC-seq
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Mix of human and mouse cell lines
|
| Data processing |
Fastqs were generated using CellRanger-ATAC mkfastq v1.1.0
Sequencing reads were aligned using CellRanger-ATAC count for the hg38 and mm10 reference genomes
For Phage libraries, phage tag abundances were quantified per barcode using a custom unix script.
Genome_build: hg38 / mm10
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 |
Sep 04, 2020 |
| 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 |
GPL19415 |
| Series (2) |
| GSE157485 |
Single cell analysis of protein epitopes and chromatin accessibility using PHAGE-ATAC [Species_Mix_GFP] |
| GSE157486 |
Single cell analysis of protein epitopes and chromatin accessibility using PHAGE-ATAC |
|
| Relations |
| BioSample |
SAMN16058329 |
| SRA |
SRX9075341 |
