|
| Status |
Public on Mar 19, 2021 |
| Title |
RSD 34 |
| Sample type |
SRA |
| |
|
| Source name |
Heart
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: wild-type Groningen rats
tissue: Heart - left ventricle
Sex: male
age: adult
treatment: Repeated Social Defeated (RSD)
|
| Treatment protocol |
Social defeat stress was based on a classical “resident–intruder” paradigm (Miczeck, 1979), The defeat sessions were repeated for 8 consecutive days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hearts were excised, flash frozen on dry ice, and punches form left ventricles were dissected. RNA was extracted using Norgen minicolumn ( Total RNA purification Kit) and quality checked via Agilent 2100 bioanalyzer assay
Libraries were prepared from 100ng of total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen GmbH). Libraries were sequenced on a NovaSeq 6000 sequencing system using an S1, 100 cycles flow cell (Illumina Inc.)
RNA-Seq (mRNA 3' Digital Gene Expression)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina novaSeq base call (BCL) files were converted in fastq file through bcl2fastq(version v2.20.0.422)
Sequence reads were trimmed using bbduk software[2] (bbmap suite 37.31) to remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6)
Alignment was performed with STAR 2.6.0a on rn6 assembly downloaded from UCSC Genome Browser website
The expression levels of genes were determined with htseq-count 0.9.1 by using Ensembl genes annotations (Version 6.0).
Individual sample counts were normalized via Relative Log Expression (RLE) using DESeq2 R library
Genome_build: rn6 genome from UCSC genome browser
Supplementary_files_format_and_content: excl file including raw gene counts values for each sample in a matrix. We remove all genes having Perc MM reads > 20% and the genes having < 1 cpm in less than n_min1 samples. All the genes not passing either of the filters are indicated in the column “Removed gene” with TRUE.
|
| |
|
| Submission date |
Mar 18, 2021 |
| Last update date |
Mar 20, 2021 |
| Contact name |
Luisa Lo Iacono |
| E-mail(s) |
luisa.loiacono@yahoo.it
|
| Organization name |
Fondazione Santa Lucia IRCCS
|
| Department |
behavioral neuroscience
|
| Lab |
115
|
| Street address |
via del fosso di Fiorano 64
|
| City |
Rome |
| ZIP/Postal code |
00143 |
| Country |
Italy |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE169181 |
The effect of Repeated Social defeat stress (RSD) on transcriptomic profiles of rat heart |
|
| Relations |
| BioSample |
SAMN18351891 |
| SRA |
SRX10379018 |
