|
| Status |
Public on Jun 30, 2021 |
| Title |
THP1.400nM.GSK032.d4.n1 [S1-39] |
| Sample type |
SRA |
| |
|
| Source name |
THP1_GSK032_400nM
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP1
cell tye: AML cell line
treatment: GSK032
dose: 400nM
time: d4
replicate: n1
|
| Treatment protocol |
Cells were plated 24 hours before treatment with either DMSO, GSK3484862, GSK3685032, DAC, or GSK3510477 then grown for the indicated time before collection.
|
| Growth protocol |
Cell lines were obtained from the American Type Culture Collection, the Deutsche Sammlung von Mikroorganismen und Zellbulturen, or AddexBio and maintained in the recommended cell culture media at 37°C in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Qiagen Rneasy Mini kit
Libraries were prepared at the NYU Medical Center Genome Technology Center
All 150 PE libraries were sequenced across 6 lanes for a total of 12 fastq samples per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
processed data file: DNMT1_AML_fpkm_THP1_table.txt
|
| Data processing |
Salmon_v0.12.0 transcript quantification
DEseq2 log2 fold change differential expression and normalized fpkm quantification
fGSEA gene set enrichment analysis
Genome_build: Human hg38
Supplementary_files_format_and_content: fpkm values for all quantifiable genes; log2 fold change values for all quantifiable genes
|
| |
|
| Submission date |
Aug 05, 2019 |
| Last update date |
Jun 30, 2021 |
| Contact name |
Shawn W Foley |
| E-mail(s) |
shawn.w.foley@gsk.com
|
| Organization name |
GlaxoSmithKline
|
| Department |
Oncology
|
| Street address |
1250 S. Collegeville Rd
|
| City |
Collegeville |
| State/province |
PA |
| ZIP/Postal code |
19426 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE135207 |
Expression profiling and methylation analysis of DNMT1 inhibitor treated AML cell lines |
| GSE135378 |
RNA-seq of DNMT1 inhibitor treated AML cell lines |
|
| Relations |
| BioSample |
SAMN12496467 |
| SRA |
SRX6657137 |
