|
| Status |
Public on Dec 31, 2018 |
| Title |
28789 |
| Sample type |
SRA |
| |
|
| Source name |
airway smooth muscle
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: asthma
treatment: vehicle
donor: 28789
tissue: airway smooth muscle
ercc_mix: 1
|
| Treatment protocol |
cells were treated with budesonide (100nM for 24h) or vehicle control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the miRNAeasy mini kit (Qiagen Sciences, Inc., Germantown, MD).
TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, Inc., San Diego, CA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
PostQC_all_sample_TPM.txt
Differential_expression_BUD_vs_vehicle_asthma.txt
Barcode: ATGTCA
|
| Data processing |
Sample 28782 was excluded from analyses due to having low reads; its corresponding vehicle sample from the same donor (28779) was therefore excluded as well
kallisto was used to obtain TPM per transcript
sleuth was used to perform differential expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: Space-delimited text files include TPM values per gene for each sample that passed QC (PostQC_all_sample_TPM.txt) and transcript-based differential expression results for pairs of samples that passed QC for the BUD vs. vehicle comparison in asthma and non-asthma (Differential_expression_BUD_vs_vehicle_asthma.txt and Differential_expression_BUD_vs_vehicle_non-asthma.txt, respectively).
|
| |
|
| Submission date |
Jan 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Blanca E Himes |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Pennsylvania
|
| Department |
Department of Biostatistics, Epidemiology and Informatics
|
| Lab |
402 Blockley Hall
|
| Street address |
423 Guardian Dr
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE94335 |
Fatal Asthma and Non-Asthma Donor-Derived Airway Smooth Muscle Transcriptome Response to Glucocorticoid Treatment |
|
| Relations |
| BioSample |
SAMN06285144 |
| SRA |
SRX2529968 |
