|
Status |
Public on Aug 09, 2023 |
Title |
RFID 933000320047161 (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 |
SAMN30616397 |
SRA |
SRX17382897 |
Supplementary file |
Size |
Download |
File type/resource |
GSM6529610_933000320047161_fragments.tsv.gz |
1.5 Gb |
(ftp)(http) |
TSV |
GSM6529610_933000320047161_fragments.tsv.gz.tbi.gz |
884.8 Kb |
(ftp)(http) |
TBI |
GSM6529610_933000320047161_singlecell.csv.gz |
4.0 Mb |
(ftp)(http) |
CSV |
GSM6529610_933000320047161_summary.csv.gz |
546 b |
(ftp)(http) |
CSV |
GSM6529610_FTL_456_M985_933000320047161_barcodes.tsv.gz |
27.5 Kb |
(ftp)(http) |
TSV |
GSM6529610_FTL_456_M985_933000320047161_matrix.mtx.gz |
90.1 Mb |
(ftp)(http) |
MTX |
GSM6529610_FTL_456_M985_933000320047161_peaks.bed.gz |
950.5 Kb |
(ftp)(http) |
BED |
SRA Run Selector![Help](/coreweb/images/long_help4.gif) |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |