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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 24, 2021 |
| Title |
Hippocampus_CE3 |
| Sample type |
SRA |
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| Source name |
Hippocampus
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: postnatal day 70
prenatal treatment: control
postnatal treatment: enrichment
tissue: Hippocampus
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| Treatment protocol |
C57BL/6 mice were exposed to ethanol via two subcutaneous injections of 2.5 g/kg ethanol in 0.15 M saline two hours apart on postnatal day 6 and 7. Control mice received 0.15 M saline volume-equivalent injections. On P21, each pup was randomly assigned to either the enriched group or standard housing control group. Enriched mice were housed with same-sex littermates in large colony cages of 2-6 individuals supplied with extra bedding, hidden food pellets, additional nest material, running wheels, hoops, ladders, as well as toys and objects of varied shape, color, texture, and size. This protocol generated mice belonging to one of four groups based on ethanol exposure and environmental enrichment: control (no ethanol nor enrichment), enriched (no ethanol), ethanol (no enrichment), and ethanol enriched.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were sacrificed via carbon dioxide asphyxiation and cervical spinal dislocation. Hippocampus was dissected, snap-frozen in liquid nitrogen, and stored at -80°C. RNA was isolated using AllPrep DNA/RNA Mini Kit (Qiagen) and stored at -80°C.
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded total RNA Library Preparation protocol with rRNA depletion using RiboZero Gold.
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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 |
Base-calling was performed using CASAVA
Paired-end reads for each sample were quantified via pseudoalignment to version 38 of the Ensembl annotation of the mouse transcriptome using kallisto with 100 bootstrap samples taken
Differential analysis of gene expression was determined using sleuth via p-value aggregation
Genome_build: mm10
Supplementary_files_format_and_content: "tpmdata" contains the Sleuth object count matrix using normalized observations in transcripts per million for each transcript detected for sample as a comma separated values file
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| Submission date |
Sep 22, 2021 |
| Last update date |
Sep 24, 2021 |
| Contact name |
Shiva M Singh |
| E-mail(s) |
ssingh@uwo.ca
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| Organization name |
Western University
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| Department |
Biology
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| Lab |
Singh
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| Street address |
1151 Richmond Street
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| City |
London |
| State/province |
ON |
| ZIP/Postal code |
N6A 5B7 |
| Country |
Canada |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE184615 |
Hippocampal transcriptome analysis following environmental enrichment in a mouse model of fetal alcohol spectrum disorder |
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| Relations |
| BioSample |
SAMN21555459 |
| SRA |
SRX12299942 |
| 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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