|
| Status |
Public on Jan 07, 2020 |
| Title |
OVCAR8 parental control-3 [272 DS-15] |
| Sample type |
SRA |
| |
|
| Source name |
OVCAR8 parental control
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: OVCAR8
phenotype: parental
treatment: control
|
| Treatment protocol |
Parental and neratinib-resistant cells were seeded in triplicate in 10-cm dishes and then treated with or without neratinib (5637 – 600 nM; OVCAR8 – 1 μM); 24h later, cells were harvested and RNA was extracted.
|
| Growth protocol |
5637NR and OVCAR8NR cells were maintained under drug-free conditions for 1 week prior to seeding.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using ReliaPrep RNA Cell Miniprep system (Promega). Total RNA was quantified using the Quant-iT Ribo-Green RNA Assay Kit (Invitrogen).
Automated Illumina Tru Seq Sample Preparation protocol was used to separate mRNA from total RNA, followed by cDNA 18 synthesis. Libraries were prepared using TruSeq® Stranded mRNA Library Prep kit (Illumina). Following quality check, the libraries were quantified using the KAPA Library Quantification Kits for Next-Generation Sequencing (Kapa biosystems), pooled and sequenced on the HiSEq3000 platform targeting 50 million paired end reads/sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
OVCARctrl3
|
| Data processing |
Quality control on raw reads was performed using FastQC.
STAR v2.5.3a used for reads mapping.
FeatureCounts v1.15.2 was used to count the number of mapped reads to each gene.
BiomaRt package was used to map mouse genes to human genes, and only uniquely mapped genes between human and mouse were kept.
Significantly differentially expressed genes with FDR-adjusted p-value≤0.01 and absolute fold-change≥2.0 were detected by DESeq2 (v1.18.1).
Genome Ontology and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway over-representation analysis was performed on differentially expressed genes using the WebGestaltR package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample.
|
| |
|
| Submission date |
Mar 22, 2019 |
| Last update date |
Jan 07, 2020 |
| Contact name |
Dhivya Sudhan |
| E-mail(s) |
Dhivya.Sudhan@UTSouthwestern.edu
|
| Organization name |
Vanderbilt University
|
| Department |
Hematology/Oncology Division
|
| Street address |
777 Preston Research Building
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232-6307 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE128730 |
RNAseq of parental and neratinib resistant 5637 and OVCAR8 cells with or withour neratinib treatment |
|
| Relations |
| BioSample |
SAMN11234200 |
| SRA |
SRX5560980 |
