|
| Status |
Public on Feb 20, 2022 |
| Title |
Saline_GFP__SG15 |
| Sample type |
SRA |
| |
|
| Source name |
Virally-infected tissue from Ventral Tegmental Area brain reion
|
| Organism |
Rattus norvegicus |
| Characteristics |
background strain: Sprague-Dawley
weight: 250-275g
genotype: wild-type
Sex: male
treatment: 10d Saline Self Administration + Virus treatment (@ d11) + 30d Abstinence
treatment: GFP Virus treatment
|
| Treatment protocol |
Animals went through either Saline or Heroin SA for 10d, and virus was injected (GFP, H3.3WT, or H3.3 Q5A) intra-VTA at 11d, tissue was collected at abstinence d30
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using trizol-chloroform extraction followed by cleanup on the RNeasy Micro Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the Illumina Truseq RNA Library Prep Kit V2 , according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
concatenated read data from 2 flow cells
|
| Data processing |
fastq files were aligned to ensembl Rnor_6.0 (GCA_000001895.4) rat reference genome using HISAT2 (Version 2.1.0) and ensembl v90.
BAM files resulting from the alignments were summarized to genes using the featureCounts (Version 2.0.1) algorithm
Expression data was normalized using RUVr from RUVseq (Version 4.1.1)followed by DESEQ2 (Version 2.11.40.6)
Differentially expressed genes (5% false discovery rate) were identified using DESEQ2 based on a model using the negative binomial distribution
Genome_build: rnor6 rat genome
Supplementary_files_format_and_content: tab-delimited text files are VST normalized counts matrix for each sample from DESEQ2 output
|
| |
|
| Submission date |
Nov 24, 2021 |
| Last update date |
Feb 20, 2022 |
| Contact name |
Sasha Leilani Fulton |
| E-mail(s) |
slf2127@columbia.edu
|
| Organization name |
Columbia University
|
| Street address |
3227 Broadway
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10025 |
| Country |
USA |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE169628 |
Histone H3 dopaminylation in ventral tegmental area underlies heroin-induced maladaptive plasticity |
|
| Relations |
| BioSample |
SAMN23428343 |
| SRA |
SRX13222219 |
