|
| Status |
Public on Oct 05, 2021 |
| Title |
Fos_dox_24h_afatinib_5uM_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
ASZ001 murine BCC cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: ASZ001
genotype: c-Fos
treatment: Dox + afatinib
|
| Treatment protocol |
Upon dox induction for 24h, cells are either treated with afatinib (5uM) or UO126 (10uM) or DMSO control for 6h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples were obtained from adherent cells using RNeasy kit from QIAGEN according to manufacturer's instructions. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Tophat used for alignment.
Homer is used to calculate raw counts and FPKM values.
deseq2 is used for differential analysis.
Genome_build: mm9
Supplementary_files_format_and_content: RNAseq_inhibitor_tx_counts.txt: Tab-delimited text file includes raw count values for each sample.
|
| |
|
| Submission date |
Feb 10, 2021 |
| Last update date |
Oct 05, 2021 |
| Contact name |
Anthony Oro |
| Organization name |
Stanford University
|
| Department |
Dermatology
|
| Street address |
269 Campus Drvie
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE166596 |
Transcriptional changes in experimentally-induced basal to squamous cell carcinoma transition (BST) upon treatment with small molecule inhibitors [ASZ_RNAseq_inhibitor] |
| GSE168376 |
C-FOS-driven basal to squamous cell transition |
|
| Relations |
| BioSample |
SAMN17863454 |
| SRA |
SRX10073601 |
