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Sample GSM718712 Query DataSets for GSM718712
Status Public on Jun 01, 2011
Title Healthy smoker (S_NuGEN)
Sample type SRA
 
Source name Large airway epithelial cells
Organism Homo sapiens
Characteristics cell type: large airway epithelial cells
gender: 1 Male, 2 Female
average age: 41.7
smoking status: 3 Current
packyears: 21.5
lung cancer: 3 No
Extracted molecule total RNA
Extraction protocol Standard Illumina mRNA-seq Protocol (Paired end 75 bp reads, fragments were 300bp, 2 50 bp adapter sequences, 2 75 bp reads, and a 50 bp insert (sd= 50bp) or prototype NuGEN Ovation RNA-seq protocol (36 bp single end reads)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description Prototype NuGEN Ovation RNA-seq Protocol, 36 bp single end sequencing
Data processing Reads were aligned to human genome build 19 using Tophat software v1.0.14 with mammalian defaults with the exception of specifying a maximum of 10 multi-reads. Gene expression measurements (RPKM, reads per kilobase per million reads) were calculated based on the alignments using Scripture software's score function. The annotation file used by Scripture software was based on Ensembl v59 (n=49,702 genes) where the union set of transcripts mapping to a single gene was used to summarize gene-level expression. The FWER corrected p-value for the observed read count across the transcript (Scripture software) was used to decide if a gene confidently expressed in a sample (p-value < 0.05 were designated as present).
 
Submission date May 02, 2011
Last update date May 15, 2019
Contact name Avrum Spira
E-mail(s) aspira@lung.bumc.bu.edu
Phone 617-638-4860
Fax 617-536-8093
URL http://www.pulmonomics.org
Organization name Boston University Medical Center
Department Pulmonary and Critical Care Medicine
Lab Pulmonomics Lab
Street address 715 Albany Street, R304
City Boston
State/province MA
ZIP/Postal code 02118
Country USA
 
Platform ID GPL10999
Series (2)
GSE29006 mRNA-seq of Human Airway Epithelial Cells
GSE29007 Human Large Airway Epithelial Cells from healthy never and current smoker and smokers with and without lung cancer
Relations
SRA SRX060174
BioSample SAMN00262799

Supplementary file Size Download File type/resource
GSM718712_S_nugen.bedgraph.gz 57.3 Mb (ftp)(http) BEDGRAPH
GSM718712_S_nugen_FPKM_Cufflinks.txt.gz 195.6 Kb (ftp)(http) TXT
GSM718712_S_nugen_RPKM_Pvalue.txt.gz 345.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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