|
| Status |
Public on Apr 25, 2018 |
| Title |
RNA5_Male_KO_3wks |
| Sample type |
SRA |
| |
|
| Source name |
male ERRg knockout kidney (3 weeks) sample 5 mRNA
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: kidney
genotype: ERRg fl/fl;Sim1-Cre
Sex: male
age: 3 weeks
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from Cre- (control) and Cre+ (ERRg KO) 3-week-old or 3-month old male or female littermate mouse kidneys were purified. RNA quality was assessed using a Bioanalyzer (Agilent).
TruSeq Stranded mRNA sample prep kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA5_Male_KO_3wks
|
| Data processing |
Alignment: Sequenced reads were aligned to the mm10 reference mouse genome using STAR
Differenial Expression Analysis: differentially expressed RNAs were identified using DESeq2 (FDR-adjusted p-value <0.01, fold change>±1.5). STAR alignment and DESeq2 analysis were executed through the RNA Express BaseSpace application (Illumina).
Visualization: bedGraph files were generated from aggregated male and female sequencing data (mice at 3 weeks of age) using HOMER which were viewed on the UCSC genome browser.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text (txt) file with differential expression and bed graphs for RNA-seq visualization.
|
| |
|
| Submission date |
Apr 25, 2018 |
| Last update date |
Apr 26, 2018 |
| Contact name |
Grant D. Barish |
| Organization name |
Northwestern University
|
| Department |
Medicine
|
| Street address |
303 E Superior Street
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE104906 |
ERRγ coordinates a transcriptional program of mitochondrial and renal reabsorptive functions implicated in kidney disease [RNA-seq] |
|
| Relations |
| BioSample |
SAMN08982142 |
| SRA |
SRX3995352 |
