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Sample GSM3602439 Query DataSets for GSM3602439
Status Public on Dec 23, 2019
Title THP1 RAD001 & OG86 Rep3
Sample type SRA
 
Source name THP1 RAD001 & OG86
Organism Homo sapiens
Characteristics cell line/sample: THP1
cell type: monocytic cell line derived from an acute monocytic leukemia patient
treatment: RAD001 (40 nM) and OG86 (250 nM) for 24 hours
Treatment protocol Cells were treated with DMSO (vehicle), RAD001 (40 nM), OG86 (250 nM) or RAD001 (40 nM) and OG86 (250 nM) for 24 hours followed by RNA isolation
Growth protocol THP1 cells were cultured in RPMI1640 supplemented with 10% FBS, 10 U/mL Penicillin, 10 µg/mL Streptomycin, 2 mM L-glutamine. Culture densities were 5x10^4 - 5x10^5 for cells in liquid culture.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from DMSO or OG86-treated THP1 AML cells using QIAshredder spin columns and an RNeasy Plus Micro Kit (Qiagen, Manchester, UK) and its quality confirmed using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description TS84_12_RAD001-OG86_3_S12
Data processing Paired-end reads were mapped to the human genome (GRCh38 Gencode release 25) with STAR version 2.4.2a with the settings --outFilterMultimapNmax 20, --outFilterType BySJout, --alignSJoverhangMin 8 and --quantMode GeneCounts using the matching feature annotation GTF file for GRCh38 Gencode release 25. Differential gene expression analysis was performed using DESeq2 version 1.20.0.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw read count values per gene for each sample
 
Submission date Feb 13, 2019
Last update date Feb 05, 2020
Contact name Tim C Somervaille
E-mail(s) tim.somervaille@cruk.manchester.ac.uk
Organization name Cancer Research UK
Department Manchester Institute
Lab Leukaemia Biology
Street address Wilmslow Rd
City Manchester
ZIP/Postal code M20 4BX
Country United Kingdom
 
Platform ID GPL18573
Series (1)
GSE126486 Genome-wide CRISPR-Cas9 screen identifies druggable synthetic lethality between LSD1 and MTORC1 in MLL-translocated AML
Relations
BioSample SAMN10924207
SRA SRX5371468

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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