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| Status |
Public on Apr 14, 2020 |
| Title |
F2_Beta3_SGM18 |
| Sample type |
SRA |
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| Source name |
Hippocampus
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| Organism |
Cavia porcellus |
| Characteristics |
generation: F2
treatment: Beta
age: post natal day 40
Sex: Female
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| Extracted molecule |
total RNA |
| Extraction protocol |
Brains were removed, and hippocampus was surgically extracted and flash frozen on dry ice. 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; Bisulfite DNA libraries were prepared from purified DNA, using the KAPA Library Prep Kit Illumina (Roche) according SeqCap Epi Enrichment System User’s guide
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| 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.
Bisulfite treated DNA Seq reads were trimmed using Trimmomatic-0.32, then aligned to the guinea pig genome (cavPor3) using bsmap-2.74 v0.12.5. Picard-tools-1.93 was used to remove duplicates. Methylation levels were determined for individual CpG sites using bsmap-2.74 with a minimal coverage of 10 reads.
Changes in methylation for 100bp windows (50bp apart) and individual CpGs were detected using the calculateDiffMeth() function from MethylKit (v.1.4.0) in R (version 3.2.3). Data were annotated using Homer v4.6 with the annotatePeaks script and CavPor3 genome.
Genome_build: cavPor3
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample- EdgeR output, Methylkit output 100bp methylatio output and single nucleotide resolution (SNR) methylation output
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| Submission date |
Jan 29, 2018 |
| Last update date |
Apr 14, 2020 |
| Contact name |
Stephen Matthews |
| Organization name |
University of Toronto
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| Street address |
1 King's College Circle
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| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5S1A8 |
| Country |
Canada |
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| Platform ID |
GPL22346 |
| Series (1) |
| GSE109765 |
The Transgenerational Effects of Prenatal Synthetic Glucocorticoids on the Hippocampus Cortex |
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| Relations |
| BioSample |
SAMN08427902 |
| SRA |
SRX3606849 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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