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Sample GSM6052955 Query DataSets for GSM6052955
Status Public on Apr 24, 2022
Title 17548T
Sample type SRA
 
Source name lung tumor
Organism Homo sapiens
Characteristics batch: B
histology: Lung Cancer
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from frozen lung tissues using TRIzol (Invitrogen) according to the manufacturer’s protocol. Only RNA samples with RNA sufficient RNA were included for analysis.
Libraries suitable for paired-ended sequencing were generated using Illumina’s TruSeq Stranded Total RNA Library Prep Kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description 17548T_S19_R1_001
Data processing The sequencing quality of each sample was assessed using FastQC.
Read- and alignment-level quality were assessed using FastQ Screen, Preseq, Picard tools, RSeQC and QualiMap.
Reads were trimmed for adapter sequences and low-quality bases using Cutadapt prior to alignment against the human reference genome, hg19, using STAR in two-pass mode with GENCODE v19 annotation
Gene expression levels were quantified using RSEM.
Assembly: Hg19
 
Submission date Apr 21, 2022
Last update date Jun 10, 2022
Contact name Josh Stone
E-mail(s) josh.stone@nih.gov, harrisc@nih.gov, khanm@mail.nih.gov
Phone 240-760-7261
Organization name National Cancer Institue
Department CCR
Lab LHC
Street address 9000 Rockville Pike
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL20301
Series (1)
GSE201221 Association of gene expression with Creatine Riboside, A Prognostic Metabolite of Metabolome Imbalance in the NCI-MD Non-Small Cell Lung Cancer Cohort
Relations
BioSample SAMN27724706
SRA SRX15657669

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

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