|
| Status |
Public on Mar 18, 2020 |
| Title |
Nfe2l1_3 |
| Sample type |
SRA |
| |
|
| Source name |
Neonatal rat ventricular cardiomyocytes (NRVMs)
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
adenovirus infected: Nfe2l1
|
| Treatment protocol |
NRVMs were treated with 8 µL adenovirus in 1 mL serum-free medium (DMEM/199 medium) per each well in a 12-well plate for 48 h before collecting RNA.
|
| Growth protocol |
Neonatal rat ventricular myocytes (NRVMs) were isolated from 1- or 2-day-old Sprague-Dawley rats with the Isolation System for Neonatal Rat/Mouse Cardiomyocytes (Cellutron, nc-6031) according to the manufacturer’s instructions. NRVMs were plated at a density of 1.5x10^5 cells/well to gelatin-coated 12-well plates and were maintained in Dulbecco’s modified Eagle’s medium (DMEM/199 medium (3:1) with 3% fetal bovine serum (FBS), and penicillin-streptomycin for 48 h before adenoviral infection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Mini Kit (QIAGEN, 74104) according to the manufacturer’s protocol.
Stranded mRNA-Seq libraries were generated using the KAPA mRNA HyperPrep Kit (Roche, KK8581) following manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
NRVM_RawCountTable.txt
NRVM_RPKMTable.txt
Nfe2l1vsGFP_edgeR.txt
|
| Data processing |
Quality control of RNA-Seq data was performed using FastQC Tool (Version 0.11.4).
Sequencing reads were aligned to mouse GRCm38 (mm10) reference genome using HiSTAT2 (Version 2.0.4) with default settings and --rna-strandness F.
Aligned reads were counted using featurecount (Version 1.6.0) per gene ID.
Differential gene expression analysis was performed with the R package edgeR (Version 3.20.5) using the GLM approach. For each comparison, genes with more than 1 CPM (Count Per Million) in at least three samples were considered as expressed and were used for calculating normalization factor. Cutoff values of absolute fold change greater than 2.0 and false discovery rate less than 0.01 were used to select differentially expressed genes between sample group comparisons. Normalized gene CPM values were used to calculate RPKM (Reads Per Kilobase per Million mapped reads) values, which were then used for heatmap plotting.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files including raw count values and RPKM values for each sample, and differential expression analysis results from edgeR.
|
| |
|
| Submission date |
Dec 19, 2019 |
| Last update date |
Mar 18, 2020 |
| Contact name |
Zhaoning Wang |
| E-mail(s) |
zhw063@health.ucsd.edu
|
| Organization name |
UC San Diego
|
| Department |
Cellular and Molecular Medicine
|
| Lab |
Bing Ren Lab
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL20084 |
| Series (2) |
| GSE142364 |
Transcriptome profiling of neonatal rat ventricular cardiomyocytes overexpressing NFYa or NFE2L1 |
| GSE142366 |
Dynamic transcriptional responses to injury of regenerative and non-regenerative cardiomyocytes revealed by single-nucleus RNA sequencing |
|
| Relations |
| BioSample |
SAMN13635363 |
| SRA |
SRX7416641 |
