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| Status |
Public on Mar 31, 2021 |
| Title |
Adult rat ventral tegmental area single-nucleus RNA-seq dataset for "An atlas of transcriptionally defined cell populations in the rat ventral tegmental area" |
| 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 adult rat brain (ventral tegmenal area, or VTA). The goal of this experiment was to define the transcriptional landscapes of distinct cell types in the VTA. Single-cell sequencing was carried out with nuclei suspensions (sorted using flow cytometry) using the 10X Genomics Chromium single cell sequencing platform.
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| Overall design |
This experiment contains 4 biological samples, each of which combined tissue collected from 3 animals of the same sex. Samples were adult rat VTA microdissections isolated from male and female rats. Tissue was lysed to allow for nuclei collection via centrifugation. 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 3สน 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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| Web link |
https://www.biorxiv.org/content/10.1101/2021.06.02.446737v1.full
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| Contributor(s) |
Phillps RA, Tuscher JJ, Black SL, Ianov L, Day JJ |
| Citation(s) |
35385745 |
| Submission date |
Mar 03, 2021 |
| Last update date |
Mar 07, 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) |
| GPL20084 |
Illumina NextSeq 500 (Rattus norvegicus) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA706368 |
| SRA |
SRP309112 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE168156_RAW.tar |
149.3 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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