|
| Status |
Public on Jul 22, 2019 |
| Title |
Nppb KO mut3_LV |
| Sample type |
SRA |
| |
|
| Source name |
HOM
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB
age: 8-12 weeks
tissue: Left ventricle
genotype/variation: Nppb KO
|
| Growth protocol |
Animal care and experiments conform to the Directive 2010/63/EU of the European Parliament. All animal work was approved by the Animal Experimental Committee of the Academic Medical Center, Amsterdam, and was carried out in compliance with the Dutch government guidelines. Myh6-MerCreMer (Sohal et al., 2001) , nTnG (JAX stock #023035) and Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/J (JAX stock #021039) mice were bred on the FVB/N background.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from left ventricular tissue of Nppb KO mutants and wildtype littermates using Tri Reagent (Sigma Aldrich) according to the manufacturer’s protocol (Sigma Aldrich) and further purified using Nucleospin RNA Clean-up Kit with DnaseI treatment (Macherey-Nagel)
cDNA was prepared with the Truseq Stranded Total RNA Library Preparation Kit (Illumina, Part# 15031048 Rev. E). Total RNA (900 ng) was purified and sheared into small fragments followed by cDNA synthesis and ligation of the adapter. The quality and size distribution of the cDNA library templates were validated with Agilent DNA 1000 on 2100 Bioanalyzer (Agilent Technologies). cDNA samples were pooled per lane of paired-end 125 bp sequencing on an Illumina HiSeq 2500 instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
CRISPR deletion in exon 2 of Nppb
Nppb-KO-RNA-seq-counts.xlsx
|
| Data processing |
RNA-seq: reads were mapped to mm10 build of the mouse transcriptome using STAR (Dobin et al., 2013).
RNA-seq: Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Nppb-KO-RNA-seq-counts.xlsx (Excel file with raw and normalized (DESeq2) count data per gene & differential expression analysis).
|
| |
|
| Submission date |
Mar 12, 2019 |
| Last update date |
Jul 22, 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 |
GPL21103 |
| Series (1) |
| GSE128196 |
Transcriptional characterization of LV of Nppb KO |
|
| Relations |
| BioSample |
SAMN11107231 |
| SRA |
SRX5509435 |
