|
| Status |
Public on Nov 30, 2020 |
| Title |
HET_Vt_M2: Herozygous Ventricles, rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
Right and left murine ventricles
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Right and left murine ventricles
genotype: Gnb5 Herozygous
|
| Treatment protocol |
Wild-type, Heterzygous and knock-out mice (n = 6 per genotype)
|
| Growth protocol |
Atria, ventricles, cerebellum, hippocampi, and cerebral cortex were excised from 18weeks-old male mice with ad-libitum access to food and water
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were dissociated in QIAzol Lysis Reagent (Qiagen) using the gentleMACS™ Dissociator (Miltenyi Biotec). Cell suspension was used to obtain total RNA. Genomic DNA contamination was removed by digestion with RNase-free Deoxyribonuclease I (DNase I) (Qiagen). RNA concentration and purity were measured by ND-1000 spectrophotometer (Thermo Scientific, Wilmington, NC, USA) and RNA integrity was verified by fragment analyzer automated CE system (Advanced Analytical Technologies, Inc).
Libraries were prepared with 350 ng total RNA using Illumina TruSeq Stranded Total RNA Library Prep.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8)
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1)
Remaining reads were further filtered for low complexity with reaper (v. 15-065)
Reads were aligned to the Mus musculus.GRCm38.92 genome using STAR (v. 2.5.3a)
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7)
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1)
Genome_build: Mus musculus GRCm38.92
Supplementary_files_format_and_content: Tab-separated .txt files with gene-level read count estimates, computed by the htseq-count software package
|
| |
|
| Submission date |
Aug 26, 2020 |
| Last update date |
Dec 01, 2020 |
| Contact name |
Sylvain Pradervand |
| E-mail(s) |
Sylvain.Pradervand@unil.ch
|
| Phone |
+41 21 692 39 08
|
| Organization name |
UNI Lausanne
|
| Department |
CIG
|
| Lab |
DNA Array Facility
|
| Street address |
Genopode
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE156898 |
Inhibition of G-protein signaling in cardiac dysfunction of Intellectual Developmental Disorder with Cardiac Arrhythmia (IDDCA) syndrome. |
|
| Relations |
| BioSample |
SAMN15912711 |
| SRA |
SRX9008976 |
