|
| Status |
Public on Jan 14, 2022 |
| Title |
siLUC-2 |
| Sample type |
SRA |
| |
|
| Source name |
Neonatal ventricular myocytes
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: Neonatal ventricular myocytes
treatment: NRVM infected with siLUC
age: 1 day old pups
strain: Sprague Dawley
|
| Treatment protocol |
NRVMs from 3 independent cultures were infected with ad-siG3bp1 or ad-siLUC (control) for 48hrs,(knockdown of endogenous G3bp1 validated independent cultures), cells were collected and cell pellet was snap freezed according to Active Motif protocol
|
| Growth protocol |
Primary ventricular cardiomyocyte cultures from 1day old Sprague Dawley rat pups
|
| Extracted molecule |
total RNA |
| Extraction protocol |
frozed Cell pellet (active Motif protocol) was sent o Active Motif for RNA extraction
Directional Poly-A RNAseq libraries were prepared and sequenced as P42 (42-bp paired-ends reads) on Illumina NextSeq 500 by Active Motif
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
02_4444Rutgers_siLuciferase-control-2_RNAseq_rn_i25
|
| Data processing |
RNAseq analsyis done by Active Motif (Data Explain file attached in Pdf format). Some steps are briefly described below
Paired-end 42bp sequencing reads mapped to the genome (rn6) using STAR algorithm, alignment stored in BAM format
The number of fragments overlapping predefined genimocfeatures of inters are counted. Only reads that have both ends aligned are counted. Gene anotations used were obtained from Subread package (originally from NCBI RefSeq)
DESeq2 is used to identify statisticaly significant differential genes. Data normaliation: DESeq2 expects un-normalized count matirx of sequencing grafments. The model internally corrects for library size using their median-of-ratios method.
After dfferential test has been applied, the p-value is caluclated for each gene and adjusted to control the number of false positives by multiple testing adjustment procedure. DESeq2 filters out genes with low counts by independent filtering, using average counts of each gene (baseMean), across all samples and omits genes with average normalized counts below the filtering threshold. This threshold is automatically determined to maximize detection power at a specificed false discovery rate (FDR).
Genome_build: rn6
|
| |
|
| Submission date |
Sep 20, 2021 |
| Last update date |
Jan 14, 2022 |
| Contact name |
Danish Sayed |
| E-mail(s) |
sayeddh@njms.rutgers.edu
|
| Phone |
(973) 972-5243
|
| Organization name |
Rutgers-NJMS
|
| Department |
CBMM
|
| Lab |
MSB G 626
|
| Street address |
185 south orange avenue
|
| City |
Newark |
| State/province |
NJ |
| ZIP/Postal code |
07103 |
| Country |
USA |
| |
|
| Platform ID |
GPL20084 |
| Series (1) |
| GSE184441 |
G3bp1-miR-1 axis regulates cardiomyocyte hypertrophy |
|
| Relations |
| BioSample |
SAMN21520650 |
| SRA |
SRX12260696 |
