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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 29, 2023 |
| Title |
Mouse mPFC, CONTROL-1_biol rep 1 |
| Sample type |
SRA |
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| Source name |
Brain, adult, medial prefrontal cortex
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| Organism |
Mus musculus |
| Characteristics |
tissue: Brain, adult, medial prefrontal cortex
treatment: vehicle-only (corn oil with 5% DMSO; daily i.p. injections) treatment for 2 days
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
For experiments in organotypic tissue cultures, 5-6 cultures of the same mouse were collected and used per sample. For in vivo experiments, the mPFC of treated and untreated adult mice was dissected and the mPFC of the left hemisphere was used as one sample. In experiments with human material, the tissue of each patient was seen as one biological sample. RNA was isolated using the Monarch® Total RNA Miniprep Kit (#T2010S; New England Biolabs) according to the manufacturer's instructions. RNA quantity and quality were assessed using an Agilent RNA 6000 Pico Kit (#5067-1513; Agilent) with a 2100 Bioanalyzer (#G2939BA; Agilent). After RNA isolation from TTX-treated tissue cultures, library preparation and RNA sequencing was performed using the genome sequencer Illumina HiSeq technology in NovaSeq 6000 S4 PE150 XP sequencing mode (service provided by Eurofins). After RNA isolation from the mPFC of mouse in vivo experiments and human neocortical samples, poly(A)- selection was performed using a poly(A)-selection mRNA magnetic isolation module (#E7490; New England Biolabs) according to the manufacturer’s instructions. For non-directional library preparation, NEBNext Ultra II RNA Library Preparation Kit for Illumina (#E7770; New England Biolabs) was used.
After fragmentation and adaptor ligation, dual index primers (New England Biolabs, #E7600S) were ligated in a library amplification step using 10 PCR cycles. Libraries were finally cleaned up with 0.8X SPRI beads following a standard bead purification protocol. Library purity and size distribution were assessed with a High Sensitivity DNA assay on a Bioanalyzer instrument (Agilent). We quantified the libraries using the NEBNext Library Quant Kit for Illumina (New England Biolabs, #E7630) based on the mean insert size provided by the Bioanalyzer. A 10 nM sequencing pool (120 µl in Tris-HCl, pH 8.5) was generated for sequencing on the NovaSeq6000 sequencing platform (Illumina; service provided by CeGaT GmbH, Tübingen, Germany). We performed a paired-end sequencing with 100 bp or 150 bp read length.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Data analysis was performed at the Galaxy platform (usegalaxy.eu; (Galaxy, 2022)). All files contained more than 10 M high-quality reads (after mapping to the reference genomes) with a phred quality of at least 30 (>90% of total reads).
RNA sequencing data were uploaded to the galaxy web platform (public server: usegalaxy.eu; Afgan et al., 2018; Jalili et al., 2020; Afgan et al., 2016) and transcriptome analysis was performed using the Galaxy platform in accordance with the reference-based RNA-seq data analysis tutorial (Batut et al., 2021).
Adapter sequences, low quality, and short reads were removed via the CUTADAPT tool.
Reads were mapped using RNA STAR with the mm10 (Mus musculus) or the hg38 (Human) reference genome.
The evidence-based annotation of the mouse genome (GRCm38), version M25 (Ensembl 100) or the human genome (GRCh38), version 40 (Ensembl 106) served as gene model (GENCODE). For an initial assessment of gene expression, unstranded FEATURECOUNT analysis was performed from RNA STAR output.
Assembly: mm10
Supplementary files format and content: RNA STAR output (mapped BAM-files)
Supplementary files format and content: FEATURE COUNT output (tabular files)
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| Submission date |
Sep 26, 2023 |
| Last update date |
Sep 29, 2023 |
| Contact name |
Maximilian Lenz |
| E-mail(s) |
lenz.maximilian@mh-hannover.de
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| Organization name |
Hannover Medical School
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| Department |
Institute of Neuroanatomy and Cell Biology
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| Street address |
Carl-Neuberg-Straße 1
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| City |
Hannover |
| ZIP/Postal code |
30625 |
| Country |
Germany |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE244095 |
Antiepileptic medication induces homeostatic synaptic plasticity in pyramidal neurons of the adult human neocortex |
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| Relations |
| BioSample |
SAMN37547408 |
| SRA |
SRX21896271 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7806582_1-CONTROL_1_FEATURECOUNT.tabular.txt.gz |
256.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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