|
| Status |
Public on Mar 08, 2019 |
| Title |
SAN-adult-2 |
| Sample type |
SRA |
| |
|
| Source name |
SAN tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: sinoatrial node
developmental tissue: Adult
cell population: dissected using VENUS fluorescence as guide
|
| Growth protocol |
Human + adult and fetal mouse E17.5 SAN and working myocardium tissue was obtained in strict accordance with the Academic Medical Center Amsterdam and the Aix Marseille University
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from isolated SANs and chamber myocardial cells was obtained using the Nucleospin RNA XS isolation kit (Bioke, MN 740902.50), according to manufacturer’s protocol. The quality of total RNA was assessed by micro-electrophoresis on acrylamide gel (Agilent 2100 Bioanalyser, Agilen).
RNA template was processed with the Ovation V2 RNA-seq system (Nugen, 7102-32), according to manufacturer’s protocol. Libraries were generated using the Ovation Ultra-low system V2 1-96 (Nugen, 0344NB-A01). Amplified cDNA was bead-purified (AmpureXP, Beckman-Coulter).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500 Genetic Analyzer |
| |
|
| Description |
processed data file: VENUS_vs_KATUSHKA_adult_RNA-seq_mm10.xlsx
|
| Data processing |
Reads were mapped to mm10 or hg19 build of the mouse and human transcriptome, respectively, using STAR (Dobin et al. 2013).
Reads generated with SOLID sequencing were converted to fastqsanger with FASTQ Groomer and and aligned with TopHat using default settings
Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love, Huber, and Anders 2014).
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: Excel files with normalized (DESeq2) count data per gene & differential expression analysis: VENUS_vs_KATUSHKA_E17.5_sorted_counts_mm10.xlsx; VENUS_vs_KATUSHKA_adult_RNA-seq_mm10.xlsx; SAN_vs_RA_counts_hg19.xlsx
|
| |
|
| Submission date |
Jan 31, 2019 |
| Last update date |
Mar 08, 2019 |
| Contact name |
Vincent M. Christoffels |
| E-mail(s) |
v.m.christoffels@amsterdamumc.nl
|
| Phone |
0205667821
|
| Organization name |
Amsterdam UMC
|
| Department |
Medical Biology
|
| Lab |
Vincent Christoffels
|
| Street address |
Meibergdreef 15 K2-159
|
| City |
Amsterdam |
| State/province |
N/A (NA) |
| ZIP/Postal code |
1105 AZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16790 |
| Series (1) |
| GSE125932 |
Transcriptome analysis of mouse and human sinoatrial node cells reveals a conserved genetic program |
|
| Relations |
| BioSample |
SAMN10850782 |
| SRA |
SRX5314281 |
