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Series GSE81486 Query DataSets for GSE81486
Status Public on May 28, 2018
Title Expression profiling by small RNA-seq for identifying miRNA associated with epithelial-mesenchymal transition and acquired resistance to ALK inhibitors
Organism Homo sapiens
Experiment type Non-coding RNA 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 small RNA-seq based miRNA expression profiling.
Overall design miRNA-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 using the mirVana miRNA isolation kit (Ambion). Small RNAs (20 - 30 nt) were purified from 15% Novex TBE-Urea gel (Invitrogen) and ligated first with the 5’ RNA adaptor and then with the 3’ RNA adaptor provided by Illumina TruSeq small RNA sample preparation protocol. In each step, the ligated product was PAGE-gel purified. After first-strand synthesis and 11 cycles of PCR amplification, the product was PAGE-gel purified. Sequencing was performed in single end reads (75 bp) using NextSeq 500 platform (Illumina).
Contributor(s) Kim J, Kim S, Kim M, Yun M, Lim S, Cho B
Citation(s) 29669761
Submission date May 16, 2016
Last update date May 15, 2019
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)
GSM2154768 PR-NT-1_miRNA-seq
GSM2154769 PR-NT-2_miRNA-seq
GSM2154770 LR-NT-1_miRNA-seq
This SubSeries is part of SuperSeries:
GSE81487 Epithelial-mesenchymal transition and acquired resistance to ALK inhibitors
BioProject PRJNA321746
SRA SRP075255

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE81486_RAW.tar 150.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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