|
| Status |
Public on May 07, 2024 |
| Title |
TT1/ Tipifarnib treated TAC 1 |
| Sample type |
SRA |
| |
|
| Source name |
Serum
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Serum
cell line: Extracellular vesicles
genotype: WT
strain: C57BL6J
Sex: Male
treatment: Tipifarnib treated TAC
|
| Treatment protocol |
Tipifarnib 10mg/kg body weight of mice and TAC surgery
|
| Growth protocol |
No culture - Serum used
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Rneasy mini kit (Qiagen), ≥2µg total RNA was used for the construction of the sequencing library
Illumina mRNA seq TruSeq
Small RNA-Seq uses kits that specifically recognize the 5' and 3' ends of RNA after processing by DICER
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Small RNA sequence for serum extracellular vesicles
|
| Data processing |
next-generation sequencing using an Illumina NovaSeq platform and 2x150bp paired-end reads.
~350M raw paired-end reads per lane
FASTQ files, data QC, trimming, mapping, differential small RNA expression analysis, and novel small RNA discovery
DEseq was used to analyze the differentially expressed genes (DEG) for samples with biological replicates.
Fold change ≥2 and FDR>0.05 were set as screening criteria. miRNAs enrichment analyses of upregulated and downregulated genes were performed using KEGG and GO databases.
Assembly: not provided
Supplementary files format and content: Excel Workbook
|
| |
|
| Submission date |
Apr 29, 2024 |
| Last update date |
May 07, 2024 |
| Contact name |
Vandana Mallaredy |
| E-mail(s) |
tuj39930@temple.edu
|
| Phone |
732-614-9345
|
| Organization name |
Temple University
|
| Department |
Aging + Cardiovascular Discovery Center
|
| Lab |
Kishore Lab
|
| Street address |
3500 N Broad St, MERB 983
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19140 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE266185 |
Tipifarnib Reduces Circulating Extracellular Vesicles and Protects Against Pressure Overload-mediated Cardiac Remodeling and Dysfunction |
|
| Relations |
| BioSample |
SAMN41127510 |
| SRA |
SRX24402770 |
