|
Status |
Public on Jun 30, 2021 |
Title |
THP1.0nM.DMSO.d6.n1 [S1-50] |
Sample type |
SRA |
|
|
Source name |
THP1_DMSO_0nM
|
Organism |
Homo sapiens |
Characteristics |
cell line: THP1 cell tye: AML cell line treatment: DMSO dose: 0nM time: d6 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.
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|
|
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
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|
|
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 |
SAMN12496497 |
SRA |
SRX6657016 |