|
| Status |
Public on May 16, 2022 |
| Title |
P1 ctrl (biological replicate 2) |
| Sample type |
SRA |
| |
|
| Source name |
neonatal cardiomyocytes
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: postnatal-day-1 (P1)
genotype: ctrl
cell type: neonatal cardiomyocytes
treatment: ctrl
|
| Treatment protocol |
48 hours later, medium was replaced and cells were starved with medium without serum for 24h
|
| Growth protocol |
Cardiac cells were isolated by multiple enzymatic digestion of postnatal-day 1 (P1) mouse hearts with pancreatin and collagenase. Cardiomyocyte were purified using the immuno-magnetic cell sorting MACS Neonatal Isolation System (130-100-825, Miltenyi biotech) and cultured in gelatine-coated (0.1%, G1393, Sigma) wells with DMEM/F12 (Aurogene) supplemented with L-glutamine, sodium pyruvate, non- essential amino acids, penicillin, streptomycin, 5% horse serum and 10% FBS at 37°C and 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed with NucleoSpin RNA II kit (Macherey Nagel); 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The softwares used for data analysis are the following (in order):
NextSeq Control Software v2.2.0.4 (base-calling)
BCL to FASTQ file converter bcl2fastq (demultiplexing)
cutadapt v1.16 (Trimming)
FastQC v0.11.7
multiqc v1.5
STAR v2.5.4a (Alignment)
featureCounts v1.6.2 (Counting)
DESeq2 v1.18.1 (Differential expression)
Assembly: mmu_GRCm38.90_ERCC_SIRV
Supplementary files format and content: tab-delimited text files include raw gene counts
|
| |
|
| Submission date |
May 13, 2022 |
| Last update date |
May 17, 2022 |
| Contact name |
Gabriele D'Uva |
| E-mail(s) |
gabrielematteo.duva2@unibo.it
|
| Organization name |
University of Bologna
|
| Street address |
via Massarenti 9
|
| City |
Bologna |
| ZIP/Postal code |
40138 |
| Country |
Italy |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE202968 |
Effect of cardiomyocyte-specific deletion of glucocorticoid receptor on gene expression of cultured neonatal cardiomyocytes |
| GSE203021 |
Effect of glucocorticoid receptor deletion on gene expression of cardiomyocytes at neonatal and early postnatal stages |
|
| Relations |
| BioSample |
SAMN28233879 |
| SRA |
SRX15262283 |
