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Series GSE81484 Query DataSets for GSE81484
Status Public on May 28, 2018
Title Gene expression profiling study by RNA-seq for identifying genes associated with epithelial-mesenchymal transition and acquired resistance to ALK inhibitors
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Treatment with ALK tyrosine kinase inhibitors often elicits profound initial antitumor responses in ALK fusion-positive patients with lung adenocarcinoma. However, patients invariably develop acquired resistance to ALK inhibitors. In this study, we aimed to identify molecular events that limit the response to ALK inhibition using genetic and epigenetic approaches. To identify novel mechanisms of acquired resistance to ALK inhibitors, we established in vitro models of acquired resistance to ceritinib using H3122 cell. For in vitro model, H3122 parental cells, ceritinib-treated resistant cells, and non-resistant cells that combinely treated with certinib and panobinostat were used for RNA-seq based gene expression profiling.
Overall design RNA-seq data of 6 samples, two H3122 parental cells, two ceritinib-treated resistant cells, and two non-resistant cells that combinely treated with certinib and panobinostat, were generated. Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (2x75 bp) using NextSeq 500 platform (Illumina).
Contributor(s) Kim J, Kim S, Kim M, Yun M, Lim S, Cho B
Citation(s) 29669761, 35999456
Submission date May 16, 2016
Last update date Sep 20, 2022
Contact name Seon-Kyu Kim
Phone +82-42-879-8107
Organization name Korea Research Institutue of Bioscience & Biotechnology
Department Personalized Genomic Medicine Research Center
Street address 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea
City Daejeon
ZIP/Postal code 305-806
Country South Korea
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (6)
GSM2154748 H3122_1_RNA-seq
GSM2154749 H3122_LR_1_RNA-seq
GSM2154750 H3122_LR_Pano_1_RNA-seq
This SubSeries is part of SuperSeries:
GSE81487 Epithelial-mesenchymal transition and acquired resistance to ALK inhibitors
BioProject PRJNA321747
SRA SRP075253

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
GSE81484_RAW.tar 1.6 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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