|
| Status |
Public on Sep 12, 2022 |
| Title |
WT1 |
| Sample type |
SRA |
| |
|
| Source name |
Extracellular vesicles from infected trophoblast stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Trophoblast stem cells
rna population: Extracellular vesicle RNA
condition: Infected
treatment: Listeria monocytogenes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol Reagent method (Thermo Fisher Scientific)
Illumina Nextera XT library was used for sequencing library preparation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Used Galaxy web platform
Sequencing adopter and low qualitiy bases were trimmed using Trimmomatic
Processed reads were mapped to the mouse reference genome using HISAT2
Gene expression of mapped reads were measured using featureCounts
DESeq2 was used for differential gene expression analysis
Assembly: mm10
Supplementary files format and content: excel file includes read counts for each sample
|
| |
|
| Submission date |
Sep 08, 2022 |
| Last update date |
Sep 12, 2022 |
| Contact name |
Jonathan Hardy |
| E-mail(s) |
hardyjon@msu.edu
|
| Organization name |
Michigan State University
|
| Department |
Microbiology and Molecular Genetics
|
| Lab |
Hardy
|
| Street address |
775 Woodlot Drive
|
| City |
East Lansing |
| State/province |
Michigan |
| ZIP/Postal code |
48840 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE212928 |
Listeria monocytogenes infection alters content and function of extracellular vesicles produced by trophoblast stem cells |
|
| Relations |
| BioSample |
SAMN30727381 |
| SRA |
SRX17491016 |
