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Sample GSM4007086 Query DataSets for GSM4007086
Status Public on Jun 30, 2021
Title THP1.3.2nM.GSK032.d4.n1 [S1-36]
Sample type SRA
 
Source name THP1_GSK032_3.2nM
Organism Homo sapiens
Characteristics cell line: THP1
cell tye: AML cell line
treatment: GSK032
dose: 3.2nM
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 SAMN12496470
SRA SRX6657134

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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