|
| Status |
Public on Apr 13, 2020 |
| Title |
Experiment 2 |
| Sample type |
SRA |
| |
|
| Source name |
Uterine artery
|
| Organism |
Rattus norvegicus |
| Characteristics |
condition: Pregnant, Gestational Day 20
age: 10-12 weeks old
diet: Tekla drodent diet # 2020X
|
| Treatment protocol |
Non pregnant (diestrus) and Timed Pregnant ( Gestational Day 20) were used in the study (3 per group)
|
| Growth protocol |
Sprague-Dawley rats were purchased from Envigo laboratories and were maintained on 12 L/12 D cycles in a temperature-controlled room (23°C) and provided with food (Teklad global rodent diet # 2020X) and water ad libitum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA form the uterien arteries were performed according to the manufacturer's instructions.
The rRNA depleted total RNA was reverse transcribed, fragmented, and 3’ end repaired, after adding a “dA” base to the 3’ end, the Illumina adapter was ligated to the double strand cDNA. The adpter ligated library was then amplified using Illumina’s proprietary amplification primers. Completed libraries were qualified on Agilent 2100 Bioanalyzer for concentration, fragment size distribution between 400~600 bp
paired end RNA- seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Sprague Dawley rats
|
| Data processing |
Image analysis and base calling was performed using Solexa pipeline V1.8 (Off-Line Base Caller software, version 1.8)
Reads (pass Solexa CHASTITY quality filter) were aligned to Rat reference genome (ENSEMBL build RNO6) and Rat transcriptome (ENSEMBL build RNO6.0.98) using Hisat2 and transcript abundances for each sample was estimated with StringTie.
The gene expression level (FPKM value) and significant changes in gene expression was then calculated using R package Ballgown
rMATS was used to detecting alternative splicing events and plots.
Genome_build: Rat reference genome (ENSEMBL build RNO6) ) and Rat transcriptome (ENSEMBL build RNO6.0.98)
Supplementary_files_format_and_content: tab-delimited text matrix files with gene and transcript FPKM values along with fold change differences
|
| |
|
| Submission date |
Jan 08, 2020 |
| Last update date |
Apr 13, 2020 |
| Contact name |
Sathish Kumar |
| E-mail(s) |
sathish.kumar@wisc.edu
|
| Phone |
6082651046
|
| Organization name |
University of wisconsin Madison
|
| Department |
School of Veterinary Medicine
|
| Lab |
Comparative Bio-sciences
|
| Street address |
2015 Linden drive
|
| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL24688 |
| Series (1) |
| GSE143327 |
Genome-wide transcriptome and alternative splicing changes in pregnant rat uterine arteries |
|
| Relations |
| BioSample |
SAMN13780983 |
| SRA |
SRX7525004 |
