|
| Status |
Public on Apr 03, 2024 |
| Title |
G2 |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
cell line: Kras G12D p53-/- Keap1 R470C
cell type: CD45+ and lung tumor
genotype: C57BL/6J
treatment: DRP-104 +/- Anti-PD1
|
| Treatment protocol |
2 mice (G1 vs G2) per treatment arm: Isotype + Vehicle (HT4), DRP-104 + Isotype (HT2), anti-PD1 + Vehicle (HT3), and DRP-104 + anti-PD1 (HT1). Mice were treated for 5 days then lungs were collected for analysis
|
| Extracted molecule |
other |
| Extraction protocol |
CD45+ and tumors (GFP+) were sorted from lungs digested into a singlce cell suspension. Single cells were encapsulated in gel-beads=in emulsion using the 10x controller with a chromium single cell 5'GEM library and gel bead kit
ECCITE-seq and hashing protocol described by Stoeckius et al, Mimitou et al, Buus et al was used to generate an antibody-derived tag(ADT/hashtag oligo (HTO) library, a 5' gene expression library, and a VDJ-TCR library
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Cellranger v6.0.1 count and aggr functions to aggregate reads across sequncing lanes into a single set of barcodes.tsv.gz, features.tsv gz and matrix.mtx.gz
Supplementary files format and content: Cell Ranger output files
Library strategy: ECCITE-seq
|
| |
|
| Submission date |
Jul 17, 2023 |
| Last update date |
Apr 03, 2024 |
| Contact name |
Alireza Khodadadi-Jamayran |
| Organization name |
New York University, NYU Langone Medical Center
|
| Department |
Division of Advanced Research Technologies (DART)
|
| Lab |
Applied Bioinformatics Laboratories (ABL)
|
| Street address |
550 1st Ave, MSB 304
|
| City |
New York City |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE237592 |
Glutamine antagonist DRP-104 suppresses tumor growth and enhances response to checkpoint blockade in KEAP1 mutant lung cancer |
|
| Relations |
| BioSample |
SAMN36505351 |
| SRA |
SRX21051572 |
