|
| Status |
Public on Oct 22, 2020 |
| Title |
C-4h-IL3-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Eosinophils
|
| Organism |
Homo sapiens |
| Characteristics |
individual: subject 3
condition: allergy and mild asthma
cell type: Blood eosinophils
treatment: treated with IL-3 for 4h
|
| Treatment protocol |
Eosinophils were cultured with IL-3 (2 ng/ml) for 4 or 20 hours before lysis and total RNA extraction
|
| Growth protocol |
Peripheral blood eosinophils were cultured in RPMI with 10% fetal bovine serum (FBS) at 1 million cells/ml.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from eosinophils using the RNeasy Mini Kit (Qiagen, Valencia, CA) and treated with DNase (RNase-free DNase kit, Qiagen). RNA samples were submitted to the University of Wisconsin-Madison Biotechnology Center (Madison, WI) for RNA quality and integrity evaluation via Agilent 2100 Bioanalyzer platform (Agilent Technologies), library preparation and sequencing.
Takara SMARTer v4 Ultra-Low Input RNA / NexteraXT Library Prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
RNA-seq (1x100 bases; duplicate runs, 30 million reads per sample) was carried out using Illumina HiSeq 2500 platform and Illumina Casava software was used for basecalling and generating sequence data at UW-Madison Biotech Center.
SeqMan Ngen (v.15) and ArrayStar with Qseq module (v.15) software packages (DNAStar, Madison, WI) were used to map sequence reads to human reference genome (GRCh38) and perform gene expression analysis; two raw data files (fastq format, L001 and L002) obtained for each total RNA sample from two lanes of a HiSeq 2500 flowcell, were analyzed as technical replicates to generate a single normalized abundance measurement file per each sample.
Genome_build: Human reference genome, version GRCh38
Supplementary_files_format_and_content: Normalized log2 transformed RPKM (Reads Per Kilobase per Million mapped reads) values are presented in the processed data file (Microsoft Excel metadata spreadsheet).
|
| |
|
| Submission date |
Oct 21, 2020 |
| Last update date |
Oct 22, 2020 |
| Contact name |
Yury A Bochkov |
| E-mail(s) |
[email protected]
|
| Phone |
608-263-8553
|
| Organization name |
University Of Wisconsin-Madison
|
| Department |
Pediatrics
|
| Street address |
600 Highland Ave, K4/945 CSC
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53792-9988 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE159782 |
Increased IL-6 Trans-Signaling in the Airways After an Allergen Challenge |
|
| Relations |
| BioSample |
SAMN16511652 |
| SRA |
SRX9333023 |
