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| Status |
Public on Jul 05, 2024 |
| Title |
NAc_Npbwr1-OE, rep4 |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: Brain
region: Nucleus accumbens
strain: C57BL/6J
genotype: Npbwr1-OE
Sex: female
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| Treatment protocol |
1) At four time points (4h, 10h, 16h, 22h), mice were intraperitoneally (i.p.) injected with 7.5 mg/kg caffeine (#, C0750, Sigma) or saline at an injection volume of 10ml/kg body weight and tested 2h later. NPB ((#CSB-MP015971HU-100, Cusabio) was injected at doses of 1, 3, and 10 nM into the NAc. NPB was diluted in ddH2O up to 100 nM and then diluted with artificial cerebrospinal fluid, which also served as a control. CYM50769 (#1067-25mg, Sigma Aldrich) was injected into the NAc at doses of 0.1 – 10 μM. CYM50769 was diluted in DMSO up to 100 μM and then diluted in artificial cerebrospinal fluid, which also served as a control solution containing the proper concentration of DMSO (#3525, Tocris). 2) Bilateral stereotaxic surgery into the NAc was essentially performed as described (doi: 10.1038/nm.4386). Viruses were utilized at concentrations from 2 x 10^10 (OE) to 6 x 10^11 (GFP ctrl) particles * 0.1ml: pAAV.1-CAG-GFP (#37825, Addgene), OE-Npbwr1-GFP: pAAV-CAG-GFP-P2A-Npbwr1-WPRE1. Npbwr1-regulating AAVs were custom-made by Charitè viral vector core, Berlin, Germany. All AAVs were serotype 1.
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| Growth protocol |
Mice were at least 8 weeks old and were housed in a 12L:12D light cycle.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA extraction involved resuspension in Trizol and chloroform precipitation, followed by washing with isopropanol and 75% ethanol. Subsequently, cDNA conversion was performed using the GoScript™ Reverse Transcriptase kit (#A5001, Promega).
1) Library was prepared using Novogene NGS RNA Library Prep Set (PT042) according to manufacturer instructions. 2) Libraries were prepared from 500 ng of input material (total RNA) using NEBNext Ultra II Directional RNA Library Preparation Kit in combination with NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Multiplex Oligos for Illumina (Unique Dual Index UMI Adaptors RNA) following the manufacturer's instructions (NewEngland Biolabs).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Npbwr1-OE.N4
NAc-Npbwr1-counts.tsv.gz
NAc-Npbwr1-tpm.tsv.gz
NAc-Npbwr1-vsc.tsv.gz
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| Data processing |
Sequence information was converted to FASTQ format using bcl2fastq v2.20.0.422
Raw data was quality trimmed and clipped for Illumina universal adapter. Potential sequencing errors were detected and corrected using Rcorrector and rRNA fragments have been depleted using SortMeRNA.
Reads were mapped on GRCm38 (mm10) genome reference using segemehl, if applicable deduplicated for over-amplified PCR fragments via Unique Molecular Identifiers using UMI-tools and quantified on Ensembl v102 derived gene annotation utilizing featureCounts. Variance stabilized counts were inferred by DESeq2.
Assembly: mm10 (Ensembl v102)
Supplementary files format and content: Tab delimited text files include raw, variance stabilized and TPM normalized read counts for each sample.
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| Submission date |
Jul 05, 2024 |
| Last update date |
Jul 05, 2024 |
| Contact name |
Konstantin Riege |
| E-mail(s) |
konstantin.riege@leibniz-fli.de
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| Organization name |
Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
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| Street address |
Beutenbergstraße 11
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| City |
Jena |
| ZIP/Postal code |
07745 |
| Country |
Germany |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE271600 |
Npbwr1 signaling mediates fast antidepressant action |
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| Relations |
| BioSample |
SAMN42339207 |
| SRA |
SRX25220034 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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