|
| Status |
Public on Oct 07, 2013 |
| Title |
Smoker with Lung Cancer |
| Sample type |
SRA |
| |
|
| Source name |
Large airway epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: 2 Male, 1 Female
average age: 64.7
smoking status: 2 Former, 1 Current
packyears: 75.7
lung cancer: 3 Yes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
300ng of small molecular weight fraction (<200bp) RNA was pooled from individuals within each phenotype, never smoker (NS), current smoker (S), no cancer (NC) and cancer (C), for a total of 4 samples (900ng each). Each pooled sample was size fractioned using the Ambion flashPAGE fractionator to obtain small RNAs of 10-40nts. Small RNA sequencing libraries were created using SOLiD Small RNA Expression Kit (Ambion) starting with 200ng of the size fractionated small RNA following the manufacturer’s instructions. Libraries were sequenced on an Applied Biosystems SOLiD System to obtain 36 bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
AB SOLiD System 2.0 |
| |
|
| Description |
ABI SOLID small RNA-seq, 36 bp sequencing
|
| Data processing |
The adapter was trimmed off of the 3’ end of each read. Reads were aligned to the human genome build 19 (hg19) using Bowtie version 0.12.3 allowing up to two mismatches and limiting the number of locations a read can map to the genome to 4 or fewer. The number of reads that overlap with the genomic locations of known mature microRNA from miRBase v16 and from the miRDeep predictions for miR- 4423 was counted using BEDTools v2.9.0.
|
| |
|
| Submission date |
Oct 12, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Avrum Spira |
| E-mail(s) |
aspira@bu.edu
|
| Organization name |
Boston University
|
| Department |
Computational Biomedicine
|
| Lab |
Spira/Lenburg Lab
|
| Street address |
72 East Concord Street, E631
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL9138 |
| Series (2) |
| GSE32726 |
Identification of miR-4423 as a Primate-Specific microRNA Highly Expressed in Ciliated Airway Epithelium and Associated with Lung Cancer [high throughput sequencing] |
| GSE48798 |
Identification of miR-4423 as a Primate-Specific microRNA Highly Expressed in Ciliated Airway Epithelium and Associated with Lung Cancer |
|
| Relations |
| SRA |
SRX100649 |
| BioSample |
SAMN00738551 |
