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| Status |
Public on Jul 03, 2024 |
| Title |
NRVMs, si-RNA scramble biol rep4 |
| Sample type |
SRA |
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| Source name |
NRVM
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| Organism |
Rattus norvegicus |
| Characteristics |
cell type: NRVM
genotype: WT scramble siRNA
treatment: siRNA
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| Treatment protocol |
For siRNA knockdown, constructs were cloned into the pAd/cytomegalovirus (CMV)/V5-DEST vector (Invitrogen) and used to generate virus using the ViraPower Adenoviral Expression System (Invitrogen).
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| Growth protocol |
NRVCMs were cultured in M199 medium (Lonza) supplemented with 1% penicillin/streptomycin, heat-inactivated horse serum (Gibco), 15 µM vitamin B12 (Sigma-Aldrich), and 100 µM bromodeoxyuridine (Sigma-Aldrich). EHTs were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) low glucose (Sigma, Cat#D5546), 10% horse serum (heat inactivated, New Zealand origin, Gibco, Cat#26050088), 1% Penicillin/Streptomycin (Thermo, Cat#15070063), and 0.1% human insulin (10 mg/mL, Sigma Cat#19278).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using TRIzol™ Reagent (ThermoFisher Scientific). RNA isolation was performed with the Aurum Total RNA Mini Kit (Biorad) according to manufacturer specifications.
RNA libraries for RNA-Seq were prepared using TruSeq Stranded mRNA (Illumina) according to manufacturer's protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Raw reads were trimmed with trimmomatic (v0.36) and aligned to the human (hg19) or rat (rn6) genome using STAR with default settings.
Uniquely aligned reads were assigned to genes using htseq-count.
Raw counts were normalized with EdgeR and used to identify differentially expressed genes.
Assembly: rn6
Assembly: hg19
Supplementary files format and content: tab-delimited text file contains CPM for each sample as well as log fold change, logCPM, likelihood ratio, p-value and FDR p-value for each gene.
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| Submission date |
Nov 17, 2023 |
| Last update date |
Jul 03, 2024 |
| Contact name |
Daniel Selgrade |
| E-mail(s) |
dselgrade@gmail.com
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| Organization name |
Northwestern University
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| Lab |
McNally Lab
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| Street address |
303 E. Superior Street
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| City |
Chicago, |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
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| Platform ID |
GPL22396 |
| Series (1) |
| GSE248187 |
Innate immune activation modulates contractile and electrical dysfunction in engineered heart tissue models fordesmoplakin(DSP)cardiomyopathy. |
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| Relations |
| BioSample |
SAMN38304016 |
| SRA |
SRX22561383 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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