|
| Status |
Public on Dec 26, 2022 |
| Title |
Female, Lung, Saline, 30319-046 |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
Sex: Female
tissue: Lung
genotype: WT
treatment: Saline
|
| Treatment protocol |
Mice were sensitized and challenged with an intranasal administration of 50μL of a 25μg house dust mite, HDM, (Greer Laboratories) solution or saline.
The sensitization was performed once daily for five consecutive days, and this was followed by a daily, five successive days per week, HDM or saline challenge for three weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the RNeasy mini kit (Qiagen), quantified using a Nanodrop, and the RNA integrity was assessed using the Agilent TapeStation.
miRNA libraries were prepared using Qiagen's miRNA Library Kit following the manufacturer's protocol.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
Saline - 30319-046 - CPM
|
| Data processing |
All analysis were performed using CLC Genomics Workbench (version 12.0.2) and CLC Genomics Server (Version 11.0.4).
FASTQ files with quality scores (QS) > 30 were analyzed by CLC Genomics Workbench (version 12.0.2) using the QIAseq miRNA quantification workflow.
The deduplicated Unique Molecular Index (UMI) reads were grouped into unique search sequences and mapped to the miRNAs annotated in the miRbase v22
The miRNA expression was calculated via counting the number of distinctive UMI reads corresponding to each miRbase-annotated miRNA
miRNA expression was normalized to the sequencing depth (counts per million)
Assembly: The remaining reads were aligned to Mouse genome version: GRCm38 (Mouse Buid 38)
Supplementary files format and content: Matrix excel file containing CPM values for each sample
|
| |
|
| Submission date |
Oct 06, 2022 |
| Last update date |
Dec 26, 2022 |
| Contact name |
Mariam A Ba |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Nevada, Reno
|
| Street address |
1664 N. Virginia St
|
| City |
Reno |
| ZIP/Postal code |
89557 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE214935 |
Gene network analysis for identification of microRNA biomarkers for asthma [Lung_miRNASeq] |
| GSE214937 |
Gene network analysis for identification of microRNA biomarkers for asthma |
|
| Relations |
| BioSample |
SAMN31184970 |
| SRA |
SRX17820001 |
