|
| Status |
Public on Jan 12, 2023 |
| Title |
Fresh 1000 cell PC9:H1975 9:1 with drug treatment |
| Sample type |
SRA |
| |
|
| Source name |
Mixture of PC9 and H1975 cells (9:1)
|
| Organism |
Homo sapiens |
| Characteristics |
strain: Mixture of PC9 and H1975 cells (9:1)
Sex: pooled male and female
|
| Treatment protocol |
1 uM Gefitinib (Frontier Scientific, 501411677) or DMSO was added to culture flasks 24 hours before cells were harvested for processing. PC9 and H1975 were both treated with Gefitinib and DMSO.
|
| Growth protocol |
Cells were cultured in RPMI-1640 (Gibco #11875093) with 10% fetal bovine serum (FBS), penicillin, and streptomycin in an incubator at 37C with 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were processed according to the PIP-seq scRNA-seq workflow
PIP-seq single cell library prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Combination of the above for H1975 and PC9 cell lines
|
| Data processing |
The sample is aligned to human GRCh38.p13 with Salmon and quantified with alevin v1.2.0.
Assembly: GRCh38.p13
Supplementary files format and content: Matrices are zipped folders of 3 files: (1) sparse matrix, (2) barcodes file, (3) genes file. Raw data are gzipped fastqs, most of which have four files per sample: 2 lanes from 2 reads. Two samples were sequenced on a single lane NovaSeq run, and therefore only have the two reads from a single lane.
|
| |
|
| Submission date |
May 04, 2022 |
| Last update date |
Jan 14, 2023 |
| Contact name |
Iain Christopher Clark |
| Organization name |
University of California, Berkeley
|
| Street address |
374 Stanley Hall
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE202234 |
PIPseq on Gefitinib sensitive and resistant cell lines |
| GSE202919 |
Microfluidics-free single-cell genomics with templated emulsification |
|
| Relations |
| BioSample |
SAMN28093313 |
| SRA |
SRX15155892 |
