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| Status |
Public on Dec 06, 2019 |
| Title |
SRp_3_mRNA |
| Sample type |
SRA |
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| Source name |
Hippocampus
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| Organism |
Mus musculus |
| Characteristics |
tissue: Hippocampus
treatment: Sham
neun: positive
biol. repl.: 3
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| Extracted molecule |
total RNA |
| Extraction protocol |
24 hours after status epilepticus right hippocampi were extracted and flash frozen. Tissue was thawed in homogenization buffer and homogenized on a GentleMACS dissociator (Miltenyi). Debris was removed by density gradient centrifugation, using Debris Removal Solution (Miltenyi cat.no. 130-109-398). Nuclei were resuspended in buffer and stained with anti-NeuN-Alexa Fluor488 (Millipore cat.no. MAB377X), followed by sorting on BD FACSAria (BD Biosciences). RNA was extracted from NeuN positive nuclei, following procedures E and F.I in the mirVana miRNA Isolation Kit protocol (Ambion cat. no. AM 1560). RNA was up-concentrated using the RNA Clean & Concentrator-5 kit (Zymo Research cat.no. R1015).
SMART-Seqv4 Ultra Low InputRNA Kit for Sequencing (Takara Bio cat.no. 634891) was used to amplify 1 ng mRNA from total RNA, with 10 cycles of PCR performed. The resulting cDNA was used as input in library preparation with ThruPlex DNAseq Kit (Rubicon Genomics cat.no. R400407).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
counts_gencode.M16.txt
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| Data processing |
Trimming of fastq files with Trim Galore! (v0.4.3; default parameters)
RRBS alignment to mm10, by Bismark v0.20, powered by bowtie2
RRBS analysis of methylated/unmethylated read counts, by R package edgeR
RNA-Seq alignment and feature counts, by R package Rsubread
Genome_build: mm10
Supplementary_files_format_and_content: Bismark coverage file: Tab-delimited file with one row for each covered cytosine position in the experiment, and the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>
Supplementary_files_format_and_content: Feature counts: Tab delimited file with one row per gene. The first column has Gene ID (Ensembl), followed by one column per sample, with unnormalised counts.
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| Submission date |
Sep 27, 2019 |
| Last update date |
Dec 06, 2019 |
| Contact name |
Magnus D. Vigeland |
| Organization name |
University of Oslo
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| Department |
Medical Genetics
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| Street address |
Kirkeveien 166
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| City |
Oslo |
| ZIP/Postal code |
0424 |
| Country |
Norway |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE138100 |
Neuronal and glial DNA methylation and gene expression changes in early epileptogenesis |
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| Relations |
| BioSample |
SAMN12861449 |
| SRA |
SRX6915147 |
| 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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