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| Status |
Public on Jun 24, 2020 |
| Title |
Striatal cultured neurons single-nucleus RNA-seq dataset for "A dopamine-induced coordinated gene expression program regulates neuronal function and cocaine response" |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
This dataset contains single-nucleus RNA sequencing results from rat embryonic striatal neuronal cultures and serves as the basis for characterization of transcriptional response to dopamine (50µM), the Drd1 agonist SKF-38393 (1µM), and potassium chloride (25mM). The goal of this experiment was to define the transcriptional response to each of these stimulations across distinct cell types in cultured neurons. Single-cell sequencing was carried out on FACS-sorted nuclei isolated from these experiments using the 10X Genomics Chromium single cell sequencing platform.
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| Overall design |
This experiment contains 4 biological samples. Samples were embryonic day 18 rat primary striatal neurons cultured for 11 days in vitro prior to treatment with vehicle (neurobasal media), dopamine (50µM), the Drd1 agonist SKF-38393 (1µM), and potassium chloride (25mM) for 1hr. Neurons were cultured on 12w plates (~250,000 neurons/well), treated with described stimuli for 1hr, washed, and harvested in lysis buffer prior to isolation of nuclei via centrifugation and FACS sorting. FACS-sorted nuclei were subject to 10X Genomics GEM generation and barcoding, GEM-RT cleanup and cDNA amplication, and library construction using a Chromium Single Cell 3ʹ Reagent Kit (v3 chemistry). Libraries underwent directional, paired-end PolyA+ RNA-seq on an Illumina Next-seq 500. Each sample has multiple raw fastq files, corresponding to different sequencing lanes (e.g., L001, L002, etc) and different reads (e.g., R1, R2). Additional index files are also provided for each sample and each lane (I1).
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| Contributor(s) |
Phillps RA, Duke CG, Tuscher JJ, Zipperly ME, Ianov L, Day JJ |
| Citation(s) |
32637607 |
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| Submission date |
Sep 19, 2019 |
| Last update date |
Sep 24, 2020 |
| Contact name |
Jeremy Jason Day |
| E-mail(s) |
jjday@uab.edu
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| Phone |
205-996-8960
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| Organization name |
UAB
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| Department |
Neurobiology
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| Lab |
Day
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| Street address |
1825 University Blvd
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| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
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| Platforms (1) |
| GPL20084 |
Illumina NextSeq 500 (Rattus norvegicus) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA566455 |
| SRA |
SRP222588 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE137759_RAW.tar |
25.6 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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