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Sample GSM2774860 Query DataSets for GSM2774860
Status Public on Aug 03, 2018
Title R01-012
Sample type SRA
 
Source name Non-Small Cell Lung Cancer
Organism Homo sapiens
Characteristics disease state: Non-Small Cell Lung Cancer (NSCLC)
histology: Adenocarcinoma
histopathological grade: G2 Moderately differentiated
gender: Female
Extracted molecule total RNA
Extraction protocol Following surgical excision of tumor, necrotic debris and sampled cavitary lesions were removed to include a sufficient solid component. Next, the surgeon cut a 3-5-mm-thick slice along the longest axis of the excised tissue, which was frozen within 30 minutes of excision and later retrieved for RNA extraction
For library preparation, the TruSeq Total Stranded RNA with Ribo-Zero Reduction (Illumina) was used following manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Raw reads preprocessing and quality control:
a. Paired-end reads were filtered and trimmed using software Trimmomatic
b. Quality control before and after raw reads preprocessing was done using software FastQC
Raw reads alignment:
a. Trimmed fastq reads were aligned to human hg19 reference genome using software TopHat2 and indexed with SAMtools.
b. RNAseq alignment QC metrics were collected using software PICARD
Transcripts assembly and expression estimation:
a. Gene and isoform assembly and expression level estimation was done using Cufflinks.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing expression level for each gene per sample
 
Submission date Sep 07, 2017
Last update date May 15, 2019
Contact name Shaimaa Bakr
E-mail(s) sbakr@stanford.edu
Organization name Stanford University
Department Electrical Engineering
Street address 4450 Serra Mall, Stanford, CA 94305
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL16791
Series (1)
GSE103584 Identification of relationships between Molecular and Imaging Phenotypes in Non-small cell lung cancer using radiogenomics Map
Relations
BioSample SAMN07614298
SRA SRX3166652

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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