|
| Status |
Public on Dec 23, 2019 |
| Title |
THP1 RAD001 & OG86 Rep1 |
| 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_10_RAD001-OG86_1_S10
|
| 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 |
SAMN10924209 |
| SRA |
SRX5371466 |
