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| Status |
Public on Oct 21, 2021 |
| Title |
Intracellular_GFP_Phage |
| Sample type |
SRA |
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| Source name |
HEK293T cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
nb treatment: anti-EGFP phage nanobody
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| Treatment protocol |
Transfection using 4µg EGFP-GPI-encoding plasmid for HEK293T
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| Growth protocol |
DMEM, 10%FBS, Pen/Strep
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
NP40 lysis, see method sections for full details
Custom 10x Genomics scATAC-seq
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Description |
combEF_intra_PDT_S1_L001
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| 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
Supplementary_files_format_and_content: Per-barcode count abundance for phage library including the ATAC singlecell QC metrics; accessible chromatin fragments per atac library
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| Submission date |
Apr 21, 2021 |
| Last update date |
Oct 21, 2021 |
| Contact name |
Caleb Lareau |
| E-mail(s) |
[email protected]
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| Organization name |
Memorial Sloan Kettering
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| Street address |
417 E 68th St, Zuckerman - ZRC 1132
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL21697 |
| Series (2) |
| GSE157486 |
Single cell analysis of protein epitopes and chromatin accessibility using PHAGE-ATAC |
| GSE172921 |
Single-cell multi-modal profiling of proteins and chromatin accessibility using PHAGE-ATAC [Intracellular_GFP] |
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| Relations |
| BioSample |
SAMN18824588 |
| SRA |
SRX10654962 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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