|
| Status |
Public on Nov 16, 2023 |
| Title |
1000667_day 7 |
| Sample type |
SRA |
| |
|
| Source name |
Plasma
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: Plasma
timepoint: day 7
radiation dose: 2.2 Gy Total body irradiation
sample: 1000667
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Blood samples were taken from the animals and centrifuged to obtain plasma
TruSeq small RNA Sample Preparation kit was used for library construction
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina NextSeq 500 generated BCL files that were converted to FastQ files
FastQ files were demultiplexed using bcl2fastq2
Reads were quality filtered and adapter trimmed in silico using Cutadapt
miRDeep2 was used to generate miRNA expression count data
Data was normalized to CPM values using TMM normalization
Assembly: Sus scrofa reference genome assembly using Bowtie v2.2.3.0
Supplementary files format and content: Text file with miRNA count data
|
| |
|
| Submission date |
Oct 02, 2023 |
| Last update date |
Nov 16, 2023 |
| Contact name |
Aarti Gautam |
| E-mail(s) |
aarti.gautam.civ@health.mil
|
| Phone |
301-619-7683
|
| Organization name |
WRAIR
|
| Department |
Medical Readiness Systems Biology
|
| Street address |
503 Robert Grant Avenue
|
| City |
Silver Spring |
| State/province |
MD |
| ZIP/Postal code |
20910 |
| Country |
USA |
| |
|
| Platform ID |
GPL20983 |
| Series (1) |
| GSE244507 |
Early to Sustained Impacts of Lethal Radiation on Circulating miRNAs in a Minipig Model |
|
| Relations |
| BioSample |
SAMN37650372 |
| SRA |
SRX21970403 |
