|
| Status |
Public on Jun 25, 2022 |
| Title |
SciPlex Combo Library Well B11 |
| Sample type |
SRA |
| |
|
| Source name |
sciPlex Combinations of Drugs
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Lung Adenocarcinoma
cell line: A549
genotype: WT
treatment: Combinations of drugs at 10uM
|
| Treatment protocol |
Cells were treated with 2 drugs (or equivalent vehicle) at a concentration of 10uM at 24 hours post plating and then collected after 24 hours of treatment with compounds
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Resuspended cells were lsyed in a hypotonic buffer and fixed with a combination of DSP and 80% Methanol
Optimized sci-RNA-seq3 protocol was performed to make single cell sequencing libraries
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
sci-RNA-seq3
|
| Data processing |
First, data was demultiplexed by well. Cell barcode and UMI contained in Read1 were extracted, error corrected, and put into the header of each read.
Subsequently, reads were trimmed for polyA adaptors, mapped to the hg38 reference genome, and only transcripts mapping to the gencode annotated gene bodies were kept for further analysis
Reads were then deduplicated by UMI and assembled into a count matrix
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Jun 22, 2022 |
| Last update date |
Jun 25, 2022 |
| Contact name |
Sanjay R Srivatsan |
| E-mail(s) |
sanjays@uw.edu, sanjayrsrivatsan@gmail.com
|
| Organization name |
University of Washington
|
| Department |
Genome Sciences
|
| Lab |
Trapnell Lab
|
| Street address |
3720 15TH Ave NE Genome Sciences S Foefe Bldg
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN29254062 |
| SRA |
SRX15832585 |
