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| Status |
Public on Aug 07, 2023 |
| Title |
Single nucleus ATAC-seq datasets for "Temporally Specific Gene Expression and Chromatin Remodeling Programs Regulate a Conserved Pdyn Enhancer" |
| Organism |
Rattus norvegicus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
This dataset contains single nucleus Assay for Transposase-Accessible Chromatin (ATAC) sequencing results from rat nucleus accumbens tissue. Rats received repeated cocaine injections (20mg/kg, intraperitoneal injection), or saline injections as a control. Single-nucleus ATAC-seq was carried out with FACS-sorted nuclei using the 10X Genomics Chromium single cell sequencing platform using the Chromium Next GEM Single Cell ATAC Kit v2.
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| Overall design |
This experiment contains 4 biological samples. Samples were adult rat nucelus accumbens brain tissue isolated from rats 1hr after the final (7th) daily treatment with either saline or cocaine. Tissue was lysed to allow for nuclei collection via centrifugation. FACS-sorted nuclei were subject to 10X Genomics GEM generation and barcoding followed by preparation of snATAC-seq libraries using the Chromium Next GEM Single Cell ATAC Kit v2. Libraries underwent paired-end sequencing 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, R3). Additional index files are also provided for each sample and each lane (I1).
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| Contributor(s) |
Phillips RA, Ianov L, Day JJ |
| Citation(s) |
37333110, 37938195 |
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| Submission date |
May 30, 2023 |
| Last update date |
Dec 01, 2023 |
| 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 |
PRJNA977704 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE233754_RAW.tar |
219.0 Mb |
(http)(custom) |
TAR (of BED, MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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