|
| Status |
Public on Dec 19, 2020 |
| Title |
PC9 Day 11 |
| Sample type |
SRA |
| |
|
| Source name |
PC9
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PC9
treatment: treated with 2 µM erlotinib
timepoint: treated with erlotinib for eleven days
|
| Treatment protocol |
1x106 cells was seeded on a p100 plate. Treatment was initiated when the cells attached by adding 10 μL of 2 mM erlotinib (prepared in DMSO) to respective p100 plate containing 10 mL of media. Cells were treated for 11 days and then removed from the drug for six days and either re-treated for 2 more days (D19_ERL), or not treated (D19_DMSO). Media was changed every three days, and ~48 hours before cell collection for Drop-seq. Cells were trypsinized, centrifuged and resuspended in DMEM (no FBS), counted, and processed further for Drop-seq.
|
| Growth protocol |
Non-small cell lung carcinoma cell line PC9 (Sigma) was grown in RPMI, 5% FBS (HyClone) media containing penicillin and streptomycin in 5% CO2 at 37ºC. Cells obtained from vendor were maintained for not more than 5 passages before collection for scRNA analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Drop-seq on the single cell suspension
Nextera XT tagmentation using Illumina cat# FC-131-1096 (Drop-seq protocol)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Single cell RNA-seq was performed using Drop-seq
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Illumina paired end raw FastQ file were processed for read alignment and gene expression. Drop-seq single-cell data was analyzed using the data anlysis protocol described in Drop-seq cook-book (Macosko et al. 2015)(http://mccarrolllab.com/dropseq/) and used the Drop-seq_tools-1.13. We used STAR aligner to align the reads against genome version GRCh37.p13 hg19 (From Ensembl) and corresponding gene model is extracted from Ensembl version 74.
Quality of read and mapping were checked using the program FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Digital Gene Expression (DGE) data obtained from an aligned library is done using the Dropseq program DigitalExpression (integrated in Drop-seq_tools-1.13). Number of cells that were extracted from aligned BAM file is based on knee plot which extracts the number of reads per cell, then plot the cumulative distribution of reads and select the “knee” of the distribution.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: Tab-delimited text file. Gene expression (as count) of each gene for each extracted cell
|
| |
|
| Submission date |
Jul 25, 2019 |
| Last update date |
Dec 19, 2020 |
| Contact name |
Elizaveta V Benevolenskaya |
| E-mail(s) |
[email protected]
|
| Phone |
312-413-8947
|
| Organization name |
University of Illinois at Chicago
|
| Department |
Biochemistry and Molecular Genetics
|
| Street address |
900 S. Ashland Ave.
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60607 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE134841 |
Drug holiday expression profiling of non-small cell lung carcinoma cell line PC9 treated with erlotinib |
| GSE149383 |
Drug resistant changes at the level of single cells |
|
| Relations |
| BioSample |
SAMN12360858 |
| SRA |
SRX6589346 |
