|
Status |
Public on Aug 03, 2018 |
Title |
R01-108 |
Sample type |
SRA |
|
|
Source name |
Non-Small Cell Lung Cancer
|
Organism |
Homo sapiens |
Characteristics |
disease state: Non-Small Cell Lung Cancer (NSCLC) histology: Squamous cell carcinoma histopathological grade: G3 Poorly differentiated gender: Male
|
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.
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|
|
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
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|
|
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 |
SAMN07614282 |
SRA |
SRX3166698 |