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Sample GSM2154750 Query DataSets for GSM2154750
Status Public on May 28, 2018
Title H3122_LR_Pano_1_RNA-seq
Sample type SRA
Source name H3122 lung cancer cell line
Organism Homo sapiens
Characteristics cell line: H3122
treatment: Certinib + Panobinostat
Extracted molecule total RNA
Extraction protocol 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.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Base calling was performed by Illumina Genome Studio(V2010.1).
Reference genome sequence data from Homo sapiens were obtained from the University of California Santa Cruz Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, and SAMtools (ver. 0.1.18,
Tophat2 was applied to tissue samples for mapping reads to reference genome. The fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text format with FPKM values of transcripts
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)
GSE81484 Gene expression profiling study by RNA-seq for identifying genes associated with epithelial-mesenchymal transition and acquired resistance to ALK inhibitors
GSE81487 Epithelial-mesenchymal transition and acquired resistance to ALK inhibitors
BioSample SAMN05003689
SRA SRX1769336

Supplementary file Size Download File type/resource
GSM2154750_H3122_LR_Pano_1_FPKM.txt.gz 271.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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