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Sample GSM2285039 Query DataSets for GSM2285039
Status Public on Nov 01, 2017
Title Sample_Matthews_SGM7
Sample type SRA
Source name F1_Control_paraventricular nucleus
Organism Cavia porcellus
Characteristics generation: F1
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
BioSample SAMN05591961
SRA SRX2035027

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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