|
| Status |
Public on Aug 09, 2023 |
| Title |
RFID 933000120138414 (low), snRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Amygdala
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Heterogenous Stock (HS)
Sex: Male
tissue: Amygdala
treatment: cocaine
condition: low addition
|
| Growth protocol |
Male Heterogenous Stock (HS) rats were trained to self-administer drugs in short access conditions (2 h/day for for 10 days for cocaine) followed by long access conditions (6 h /day for cocaine) for 14 days to develop escalation of drug intake. Rats are also tested for motivation with progressive ratio sessions and for compulsivity with shock-paired sessions. Rats are classified as having low or high addiction index based on different behavioral measures. Brain punches of amygdala tissues were collected after 4 weeks of abstinence.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Brain tissues were extracted and snap-frozen. Cryosections of approximately 500 microns were used to dissect amygdala punches with a cryostat using a –20°C frozen stage. Single nuclei were isolated after tissue homogenization and iodixanol gradient purificaiton.
following the manifacture's manual for Chromium™ Single Cell 3’ v3 Library kit (10x Genomics)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Single cell RNA transcripts from amygdala
|
| Data processing |
Sequencing reads were aligned to the Ensembl Rattus norvegicus v98 Rnor_6.0 genome assembly using the 10X Cell Ranger Pipeline
Assembly: Rnor_6.0/rn6
Supplementary files format and content: Tab-separated values files and matrix files, and additional Cell Ranger output files.
Supplementary files format and content: seurat.rds: Integrated Seurat object that contains all of the snRNA-seq data across all 19 of the snRNA-seq samples.
|
| |
|
| Submission date |
Aug 31, 2022 |
| Last update date |
Aug 09, 2023 |
| Contact name |
Jessica Lu Zhou |
| Organization name |
University of California San Diego
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093-0603 |
| Country |
USA |
| |
|
| Platform ID |
GPL25947 |
| Series (2) |
| GSE212415 |
A single-cell atlas of gene expression and chromatin accessibility changes associated with cocaine addiction in the rat amygdala [snRNA-seq] |
| GSE212417 |
Cocaine addiction-like behaviors are associated with long-term changes in gene regulation, energy metabolism, and GABAergic inhibition within the amygdala |
|
| Relations |
| BioSample |
SAMN30616219 |
| SRA |
SRX17382880 |
