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| Status |
Public on Aug 09, 2023 |
| Title |
Central amygdala, snATAC-seq |
| Sample type |
SRA |
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| Source name |
Central amygdala
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Central amygdala
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For nuclei isolation, brain punches from 3 rats for each region were pooled and homogenized in homogenization buffer (0.26 M sucrose, 0.03 M KCl, 0.01 M MgCl2, 0.02 M Tricine-KOH pH 7.8, 0.001 M DTT, 0.5 mM spermidine, 0.15 mM Spermine, 0.3% NP40) using with 1ml glass Dounce homogenizers. The homogenate was filtered with a 70-um strainer filter (SP Bel-Art, cat no 136800070) and centrifuged for 5 minutes at 350 RCF. The nuclei were purified with an iodixanol gradient (Sigma-Aldrich # 92339-11-2) by layering a 25% Iodixanol-nuclei mixture on top of 30% and 40% Iodixanol solutions. After centrifugation at 4oC 3,000 RCF for 20 minutes, nuclei were collected from the 30-40% interface. Nuclei were washed in ATAC-RSB-Tween buffer (0.01 M Tris-HCl pH 7.5, 0.01 M NaCl, 0.003 M MgCl2, 0.1% Tween-20) and then resuspended in 1X nuclei buffer (10X genomics, PN 2000207).
snATAC-seq library was performed using the Chromium Next GEM Single Cell Multiome Reagent Kit A (# 1000282) following Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide (10X Genomics). After the transposition reaction, nuclei were encapsulated and barcoded. Next-generation sequencing libraries were constructed following the User Guide.
10X Genomics Multiome ATAC + Gene Expression
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Single Cell Multiome ATAC
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| Data processing |
Sequencing reads were aligned to the Ensembl Rattus norvegicus v98 Rnor_6.0 genome assembly using the 10X Cell Ranger ARC software.
Assembly: Rnor_6.0/rn6
Supplementary files format and content: Tar archives containing selected outputs from Cell Ranger ARC, including matrix files and TSV files.
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| Submission date |
Jun 20, 2023 |
| Last update date |
Aug 09, 2023 |
| Contact name |
Jessica Lu Zhou |
| Organization name |
University of California San Diego
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| Street address |
9500 Gilman Drive
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| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093-0603 |
| Country |
USA |
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| Platform ID |
GPL20084 |
| Series (2) |
| GSE212417 |
Cocaine addiction-like behaviors are associated with long-term changes in gene regulation, energy metabolism, and GABAergic inhibition within the amygdala |
| GSE235317 |
A single-cell atlas of gene expression and chromatin accessibility changes associated with cocaine addiction in the rat amygdala (snATAC-Seq Multiome) |
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| Relations |
| BioSample |
SAMN35803643 |
| SRA |
SRX20728668 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7498844_CEA.tar.gz |
2.1 Gb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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