Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 10
Release date: Nov 10 2017
Last update date: Nov 27 2018
Access: Public
Diseases: Leukemia, Large Granular Lymphocytic
Computational protocol: Picard, GATK, Subread, edgeR
Dataset link Mutational landscape of aggressive natural killer-cell leukemia and drug profiling highlight JAK-STAT signaling as a therapeutic target in NK-cell malignancies

Experimental Protocol


RNA sequencing data was obtained from natural killer and T cell lines for gene expression profiling and mutation detection in parallel with drug sensitivity profiling. The 'NK_cell_line_GEO_drug_sensitivity.txt' contains drug sensitivity scores of cell lines screened using 459 compounds. Breifly, compounds were preprinted on 384-well plates (Corning) in five different concentrations covering a 10,000-fold concentration range with an acoustic liquid handling device (Echo 550, Labcyte Inc.) and dissolved in 5 l culture medium on a shaker for 10 min. 20 l of single-cell suspension of cell lines (3,000 cells per well) were dispensed using Multi-Drop Combi peristaltic dispenser (Thermo Scientific). Plates were incubated at 37 C and 5% CO2 for 72 h after which cell viability was measured using CellTiter-Glo 2.0 reagent (Promega) according to the manufacturer s instructions with a Pherastar FS plate reader (BMG Labtech). Cell viability luminescence data were normalized to DMSO-only wells (negative control) and 100 mM benzethonium chloride-containing wells (positive control). The data were quantified using the drug sensitivity score (DSS) (Yadav et al., Scientific Reports 2014).

Repositories


GEO

GSE106391

ENA

SRP123293

BioProject

PRJNA416701

Download


Dataset Statistics

info

Citations per year

Dataset publication