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| Status |
Public on Jul 10, 2024 |
| Title |
snRNA-seq dataset for "Reelin marks cocaine-activated striatal ensembles, promotes neuronal excitability, and regulates cocaine reward" |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
This dataset contains single-nucleus RNA-seq results from rat adult nucleus accumbens tissue treated with CRISPRi machinery (hSyn-driven dCas9-KRAB-MeCP2 fusion) with a CRISPR sgRNA targeting lacZ (a bacterial gene not found in the mammalian genome; used as a non-targeting control) or Reln.
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| Overall design |
This experiment contains 8 biological samples, which represent individual rats (4 male, 4 female). Rats underwent stereotaxic surgery to transduce nucleus accumbens tissue with lentiviruses expressing CRISPRi machinery targeting lacZ (lacZ control; sample names beginning with lacZ), or Reln (sample names beginning with Reln). Two weeks following surgery, animals (4 lacZ, 4 Reln 2M/2F per group) were euthanized prior to rapid decapitation. Brains were blocked in 1mm sections, and NAc punches were obtained, flash frozen, and stored at -80°C prior to nuclei isolation. Following FACS-assisted nuclei isolation and quantification, nuclei from one rat were loaded into one GEM (gel beads in emulsion) well to generate barcoded nuclei (10× Genomics, PN-1000123, PN-1000122) on a Chromium iX instrument. Libraries were prepared according to the 10X Genomics manufacturer's recommendations, and sequenced on a NovaSeq 6000 platform to a depth of 300,000 reads per nuclei. Forward and reverse paired-end reads are denoted as "R1" or "R2" in raw file names.
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| Contributor(s) |
Brida KL, Newman CE, Ianov L, Day JJ |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jun 10, 2024 |
| Last update date |
Jul 11, 2024 |
| 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) |
| GPL25947 |
Illumina NovaSeq 6000 (Rattus norvegicus) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA1122135 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE269490_RAW.tar |
59.6 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
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