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Sample GSM2866549 Query DataSets for GSM2866549
Status Public on Feb 05, 2019
Title F1_Male_Beta_Replicate_4
Sample type SRA
 
Source name prefrontal cortex
Organism Cavia porcellus
Characteristics generation: F1
treatment: Beta
age: post natal day 40
Sex: Male
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
 
Description F1_Males_ProcessedData.txt
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 Nov 28, 2017
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)
GSE107415 The Transgenerational Effects of Prenatal Synthetic Glucocorticoids on the Prefrontal Cortex
Relations
BioSample SAMN08104000
SRA SRX3425889

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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