|
Status |
Public on Sep 20, 2018 |
Title |
LEE837_100nM_1 |
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 100nM
|
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 |
SAMN10094569 |
SRA |
SRX4718935 |