|
| Status |
Public on Jan 14, 2016 |
| Title |
GF3 medial prefrontal cortex |
| Sample type |
SRA |
| |
|
| Source name |
hand dissected medial prefrontal cortex from fresh brain tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: Swiss Webster
tissue: mPFC
age: 10 weeks
colonization status: germ-free
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using the mirVanaTM miRNA isolation kit (Ambion/life technologies) and Dnase treated (Turbo DNA-free, Ambion/life technologies) according to the manufacturers recommendations. RNA concentrations and quality were determined using Nanodrop 1000 and Bioanalyzer. Equal amounts of RNA from two to three animals were then pooled to yield four samples per group
TruSeq® Stranded mRNA Sample preparation kit was performed externaly by Exiqon, Denmark
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Base calling was achieved using standard Illumina CASAVA pipeline
Fastq-format reads were quality filtered and trimmed using Trimmomatic (v0.32)
Aligment to the mouse reference genome (GRCm38.p3) was achieved using the STAR aligner (v2.3.1u )
Ensembl database release 78 gene models were also used for counting mapped reads per gene using HTSeq-Count (v0.6.0)
Differential gene expression was calculated for pairwise comparisons using the DESeq2 R-package (v1.6.2) with default parameters. Genes with an FDR-adjusted p-value ≤ 0.1 were considered differentially regulated.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: .txt - tab delimited file with read counts for all samples (HTSeq)
Supplementary_files_format_and_content: .xlsx - Excel file with expression values, fold change, p-values and gene symbol (DESeq2) - three excel sheets in one excel workbook
|
| |
|
| Submission date |
Dec 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Roman M Stilling |
| E-mail(s) |
roman.stilling@gmail.com
|
| Organization name |
University College Cork
|
| Department |
Anatomy and Neuroscience
|
| Lab |
Neurogastroenterology
|
| Street address |
Western Road
|
| City |
Cork |
| ZIP/Postal code |
0 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE75816 |
Medial prefrontal cortex transcriptome changes in germ-free mice |
|
| Relations |
| SRA |
SRX1471709 |
| BioSample |
SAMN04326892 |
