|
| Status |
Public on Jun 01, 2011 |
| Title |
Healthy non-smoker (NS_NuGEN) |
| Sample type |
SRA |
| |
|
| Source name |
Large airway epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: large airway epithelial cells
gender: 3 Female
average age: 29.7
smoking status: 3 Never
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) |
[email protected]
|
| 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 |
SRX060173 |
| BioSample |
SAMN00262798 |
