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Sample GSM1921472 Query DataSets for GSM1921472
Status Public on Feb 01, 2016
Title Low_Pt7_anterior
Sample type SRA
 
Source name Lung tumor
Organism Homo sapiens
Characteristics cancer type: Non-small cell lung cancer (NSCLC)
perfusion group: low
Extracted molecule total RNA
Extraction protocol Human tumor samples were hormogenized in Trizol and the total RNA was extracted using RNeasy Mini Kit (Qiagen) following the manufacturer's protocol.
1-3 ug of total RNA was processed for library generation using Ovation human FFPE RNA-Seq library systems (NuGen) following the manufacturer’s protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Sequencing reads were aligned to human genome assembly hg19 by TopHat.
Transcripts were assembled and the abundance was estimated by Cufflinks.
The number of reads aligned to RefSeq annotated genes' exons were counted and further normalized to be of unit of FPKM ( number of fragments per kilo base of exon per million reads mapped) by Cuffnorm.
Genome_build: hg19
Supplementary_files_format_and_content: text file of gene read count values
Supplementary_files_format_and_content: text file of gene FPKM values
 
Submission date Oct 29, 2015
Last update date May 15, 2019
Contact name Min Ni
E-mail(s) min.ni@utsouthwestern.edu
Organization name UT Southwestern Medical Center
Department Children's Research Institute
Lab DeBerardinis Lab
Street address 6000 Harry Hines Blvd
City Dallas
State/province TX
ZIP/Postal code 75390
Country USA
 
Platform ID GPL18573
Series (1)
GSE74484 Gene expression profiling in metabolically heterogeneous human lung tumors
Relations
BioSample SAMN04225787
SRA SRX1397803

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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