|
| Status |
Public on Nov 01, 2017 |
| Title |
Sample_Matthews_SGM1 |
| Sample type |
SRA |
| |
|
| Source name |
F3_Control_paraventricular nucleus
|
| Organism |
Cavia porcellus |
| Characteristics |
generation: F3
in utero treatment: Control
age: post natal day 40
tissue: paraventricular nucleus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Brains were removed, flash frozen on dry ice. Paranvetricular nucleus was extracted via micro-punch. RNA was harvested using AllPrep RNA/DNA/microRNA Universal Extraction Kit (Qiagen Cat#80224).TruSeq RNA Library Preparation Kit V2 (Cat#RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequenced reads were aligned to cavPor3 genome assembly using TOPHAT2 and default settings
Gene read counts were generated using Genomic Alignemnts (version 1.6.3) and outliers removed using Cook's distance with default cutoffs.
Count data were normalized by residuals using RUVSeq (version 3.12.1)
Differential gene expression was assessed using EdgeR's (version 3.12.1) genral linear model likelihood ratio test and FDR-corrected p< 0.05 was considered significant.
Genome_build: cavPor3
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample- EdgeR output
|
| |
|
| Submission date |
Aug 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Matthews |
| Organization name |
University of Toronto
|
| Street address |
1 King's College Circle
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5S1A8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL22346 |
| Series (1) |
| GSE85822 |
The Transgenerational Effects of Prenatal Synthetic Glucocorticoids |
|
| Relations |
| BioSample |
SAMN05591933 |
| SRA |
SRX2035021 |
