|
| Status |
Public on Sep 06, 2022 |
| Title |
P2ry14WT-Eos-2 |
| Sample type |
SRA |
| |
|
| Source name |
WT_lung eosinophils
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
Sex: male
cell type: FACS-purified lung eosinophils
treatment condition: OVA/Aspergillus asthma model, 16 hrs after OVA challenge
|
| Treatment protocol |
Mice were sensitized twice, week apart, by oropharyngeal instillation of 50 µg OVA and 20 μg protease from Aspergillus oryzae. Seven days after the second sensitization, mice were challenged by exposing them to an aerosol of 1% OVA and lung eosinophils were purified using FACS sorting 16 h later.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using TRizol Plus reagent, followed by DNase treatment and additional cleanup step using PureLink RNA Mini kit (Thermo Fisher Scientific) according to the manufacturer's instructions.
Libraries were constructed via Illumina TruSeq RNA sample prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads were filtered to retain only those with average base quality score >20.
Reads were aligned to mm10 via STAR v2.5 (parameters: --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical).
Read counts per gene were determined by Subread featureCounts v1.5.0-p1 (parameters: -s0).
Coverage tracks were generated by STAR v2.5 (parameters: --outWigStrand Unstranded --outWigNorm None), normalized by DESeq2 size factors, then converted to bigWig format via UCSC utility bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: normalized depth tracks in bigWig format; RNAseq counts per gene in tab-delimited text format
|
| |
|
| Submission date |
May 11, 2020 |
| Last update date |
Sep 06, 2022 |
| Contact name |
Donald Nelson Cook |
| E-mail(s) |
cookd@niehs.nih.gov
|
| Phone |
(984) 287-4245
|
| Organization name |
NIEHS
|
| Department |
IIDL
|
| Lab |
Immunogenetics
|
| Street address |
111 T.W. Alexander Drive
|
| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE150347 |
Lung eosinophil RNA-Seq for P2ry14-deficient and wild-type mice |
|
| Relations |
| BioSample |
SAMN14892087 |
| SRA |
SRX8326570 |
