|
| Status |
Public on Dec 22, 2023 |
| Title |
ApoE KO HFD, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
cardiomyocytes
|
| Organism |
Mus musculus |
| Characteristics |
cell type: cardiomyocytes
genotype: ApoE KO
treatment: high fat diet
time: 7 weeks of diet
|
| Extracted molecule |
total RNA |
| Extraction protocol |
According Maxwell RSC simply/RNA kit protocol
According SMART-Seq Stranded Kit (Clontech-Takara).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.39 with the following settings (TruSeq3-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 MINLEN:36)
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR v2.7a with the following settings (--quantMode GeneCounts --readFilesIn $FASTQS --outFilterType BySJout--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate)
Read count was performed with HTSeq v0.13.5 with the following settings (f bam -m intersection-nonempty -r name -s reverse -t exon -i gene_id)
Assembly: GrCM38/mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample
|
| |
|
| Submission date |
Jul 22, 2022 |
| Last update date |
Dec 22, 2023 |
| Contact name |
Paolo Kunderfranco |
| E-mail(s) |
Paolo.Kunderfranco@humanitasresearch.it
|
| Organization name |
Humanitas Research Hospital
|
| Department |
Research
|
| Lab |
Bioinformatic Unit
|
| Street address |
Via Rita Levi Montalcini 4
|
| City |
Pieve Emanuele |
| State/province |
Milano |
| ZIP/Postal code |
20090 |
| Country |
Italy |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE209548 |
An inflammatory single-cell RNA sequencing signature driven by metabolic stress in a new mouse model of heart failure with preserved ejection fraction and its reversion by the SGLT2 inhibitor dapagliflozin [RNA-seq cardiomyocytes] |
| GSE209549 |
Single-Cell RNA Sequencing Reveals Metabolic Stress-Dependent Activation of Cardiac Macrophages in a Model of Dyslipidemia-Induced Diastolic Dysfunction |
|
| Relations |
| BioSample |
SAMN29893858 |
| SRA |
SRX16462497 |
