GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE120920 Query DataSets for GSE120920
Status Public on Nov 02, 2019
Title Integrative discovery of treatments for high-risk neuroblastoma
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Neuroblastoma (NB) cells exhibit a complex spectrum of pathway changes associated with oncogene activation, chromosome events, tumor micro-environment and super-enhancer states. So far, elucidating which pharmaceutical compounds could modulate the activation level of each known pathway in NB cells has not been feasible. We treated 2 patient-derived xenograft (PDX) NB cell lines with different chemical compounds, at 3 different doses (IC50, IC20, and IC10) and 2 time-points (6 and 24h). The whole-transcriptome of the treated cells was analyzed by a cost-effective DRUG-Seq method. Using factor analysis and supervised machine learning, the data was used to build a model that predicts the NB-specific outcome of 19,000+ drugs studied in other (non-NB) cell lines in several drug profiling databases (LINCS, CMap, DepMap).
Overall design Two patient-derived xenograft (PDX) NB cell lines treated with different chemical compounds, at 3 different doses (IC50, IC20, and IC10) and 2 time-points (6 and 24h).

Please note that the D1, D2, and D3 (in the sample titles) correspond to IC10, IC20, and IC50, respectively.
Contributor(s) Elgendy R, Almstedt E, Vanlandewijck M, Nelander S
Citation(s) 31900415
Submission date Oct 08, 2018
Last update date Jan 13, 2020
Contact name Ramy Elgendy
Organization name AstraZeneca
Street address Pepparedsleden 1
City Mölndal
State/province Göteborg
ZIP/Postal code 43153
Country Sweden
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (768)
GSM3420784 NB2_Control_CTR_rep1_6h
GSM3420785 NB2_AS601245_C1D1_rep1_6h
GSM3420786 NB2_AS601245_C1D2_rep1_6h
BioProject PRJNA495016
SRA SRP164398

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE120920_RAW.tar 127.5 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap