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Sample GSM2154770 Query DataSets for GSM2154770
Status Public on May 28, 2018
Title LR-NT-1_miRNA-seq
Sample type SRA
Source name H3122 lung cancer cell line
Organism Homo sapiens
Characteristics cell line: H3122
treatment: Certinib
Extracted molecule total RNA
Extraction protocol 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.
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
Data processing Base calling was performed by Illumina Genome Studio(V2010.1).
After TruSeq small RNA adapters were eliminated among the sequenced reads by Trimommatic software (v.0.33), the remained sequence data were mapped to the human genome (hg19) using bowtie2 (v.2.2.2).
The quantification of each miRNA was estimated using HTSeq software package.
Then, the fragments 
mapped (FPKM) of each sample was estimated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text format with FPKM values of miRNA
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
Platform ID GPL18573
Series (2)
GSE81486 Expression profiling by small RNA-seq for identifying miRNA associated with epithelial-mesenchymal transition and acquired resistance to ALK inhibitors
GSE81487 Epithelial-mesenchymal transition and acquired resistance to ALK inhibitors
BioSample SAMN05003694
SRA SRX1769352

Supplementary file Size Download File type/resource
GSM2154770_LR-NT-1_FPKM.txt.gz 23.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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