|
| Status |
Public on Aug 09, 2023 |
| Title |
RFID 933000320047651 (naïve), snATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
Amygdala
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Heterogenous Stock (HS)
Sex: Male
tissue: Amygdala
treatment: naive
condition: naive
|
| 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 |
genomic DNA |
| 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 manifacturer's manual for Chromium™ Single Cell ATAC v1 Library kit (10x Genomics)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Single cell open chromatin sites 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: signac.rds: Integrated Signac object that contains all of the snATAC-seq data across all 12 of the snATAC-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) |
| GSE212416 |
A single-cell atlas of gene expression and chromatin accessibility changes associated with cocaine addiction in the rat amygdala [snATAC-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 |
SAMN30616398 |
| SRA |
SRX17382896 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6529609_933000320047651_fragments.tsv.gz |
1.4 Gb |
(ftp)(http) |
TSV |
| GSM6529609_933000320047651_fragments.tsv.gz.tbi.gz |
875.2 Kb |
(ftp)(http) |
TBI |
| GSM6529609_933000320047651_singlecell.csv.gz |
3.8 Mb |
(ftp)(http) |
CSV |
| GSM6529609_933000320047651_summary.csv.gz |
548 b |
(ftp)(http) |
CSV |
| GSM6529609_FTL_455_M1085_933000320047651_barcodes.tsv.gz |
26.8 Kb |
(ftp)(http) |
TSV |
| GSM6529609_FTL_455_M1085_933000320047651_matrix.mtx.gz |
81.0 Mb |
(ftp)(http) |
MTX |
| GSM6529609_FTL_455_M1085_933000320047651_peaks.bed.gz |
888.5 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
