|
| Status |
Public on Jan 06, 2017 |
| Title |
AEC RNAseq_cd0c_4cca |
| Sample type |
SRA |
| |
|
| Source name |
Airway Epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
disease status: Asthma
cell type: Airway Epithelial cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
AECs were harvested via bronchial brushing and DNA/RNA was extracted consecutively using the AllPrep kit from QIAgen
Library construction protocol not provided.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
cDNA libraries were constructed using the TruSeq RNA Sample Preparation v2 according to manufacturer’s instructions
reads were mapped to the transcriptome (HG19) using BWA
sequences that overlapped with protein coding regions were determined using BEDTools
gene counts were adjusted for gene lengh
expression estimates were filtered to genes with at least 5 reads in 2 individuals and were annotated in biomart
factors of unwanted variation were identified and expression estimates were corrected for these estimates using RUVSeq
Genome_build: hg19
Supplementary_files_format_and_content: text file with normalized counts
|
| |
|
| Submission date |
Aug 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Carole Ober |
| E-mail(s) |
c-ober@genetics.uchicago.edu
|
| Organization name |
The University of Chicago
|
| Department |
Human Genetics
|
| Lab |
Ober
|
| Street address |
920 E 58TH ST
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE85567 |
DNA methylation in lung cells is a key modulator of asthma endotypes and genetic risk [RNA-seq] |
| GSE85568 |
DNA methylation in lung cells is a key modulator of asthma endotypes and genetic risk |
|
| Relations |
| BioSample |
SAMN05571275 |
| SRA |
SRX2018647 |
