|
| Status |
Public on Sep 20, 2018 |
| Title |
LEE837_1000nM_2 |
| Sample type |
SRA |
| |
|
| Source name |
U2OS
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS
cell type: osteosarcoma cell line
treatment: Homoharringtonine
|
| Treatment protocol |
U2OS cells were treated with 100nM, 1000nM and 10000nM of DMSO, AML108, AMN107, BGW675, JAA804, LEE837 and LHD510 for 12 hrs.
|
| Growth protocol |
Cells were plated down to 50-80% density 24-well plates DMEM + 10% FBS + 2mM L-Glutamine + 100 units/ml penicillin + 100 micro-g/ml streptomycin for at least 6 hours before compound treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was carried out using the Qiagen RNeasy 96 Kit.
TruSeq Stranded mRNA Library Prep kit with Poly A selection.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
LEE837 1000nM
|
| Data processing |
Aligned raw data using Star with reference genome GRCh38.
Ran HTSeq-count and RSEM to generate gene counts and tpm expression values.
Performed differential expression using DESeq2.
Genome_build: Ensembl human GRch38
Supplementary_files_format_and_content: *.genes.results.txt: Tab-delimited text files include gene counts from RSEM.
|
| |
|
| Submission date |
Sep 19, 2018 |
| Last update date |
Sep 24, 2018 |
| Contact name |
Ajamete Kaykas |
| E-mail(s) |
ajamete.kaykas@novartis.com
|
| Organization name |
Novartis
|
| Street address |
22 Windsor St
|
| City |
Cambridge |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE120222 |
Bulk RNA-seq U2OS cells treated with small molecules |
|
| Relations |
| BioSample |
SAMN10094571 |
| SRA |
SRX4718933 |
