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| Status |
Public on Dec 01, 2024 |
| Title |
Sham Control, rep2 |
| Sample type |
SRA |
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| Source name |
kidney, glomeruli
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: kidney, glomeruli
treatment: Sham Control
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| Treatment protocol |
day 0 tail vein injection of 50 mg/kg PAN, treatment thereafter 15mg/kg MP IP injection or 10mg/kg Pio PO daily. Healthy and disease controls received vehicle PO daily.
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| Growth protocol |
ad libitum water and standard chow, 12h/12h light/dark cycle, temperature/humidty controlled environment
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from the isolated glomeruli was extracted using the RNeasy Mini Kit #74104, Qiagen
350 ng total RNA was prepared to libraries with TruSeq Standard total RNA with Ribo-Zero Globin Complete kit, Illumina
To generate directional signals in RNA seq data, libraries were constructed from first strand cDNA using TruSeq Standard total RNA with Ribo-Zero Globin Complete kit from Epicentre Biotechnologies
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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 |
. Sequencing adapters matching at least 6 bases were then removed from the reads, as well as low-quality bases (<10) using v1.10 of cutadapt (https://cutadapt.readthedocs.io/en/stable/index.html)
An alignment report was also generated, using custom scripts, and manually reviewed to ensure that at least ~80% of reads aligned to the expected reference, and that at least ~50% of the reads aligned to features annotated as protein coding
Each sample was aligned to the Rnor_6.0 assembly of the Rattus norvegicus reference from the National Center for Biotechnology Information (NCBI) using version 2.5.0c of the RNA-Seq aligner STAR (http://bioinformatics.oxfordjournals.org/content/29/1/15)
Transcript features were identified from the general feature format (GFF) file that came with the assembly from the NCBI. Feature coverage counts were calculated using HTSeq (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html).
raw RNA-Seq gene expression data were normalized, and post-alignment statistical analyses and figure generation were performed using DESeq2 (http://genomebiology.com/2014/15/12/550) and custom analysis scripts written in R.
Comparisons of gene expression and associated statistical analyses were made between different conditions of interest using the normalized read counts. All fold-change values were expressed as test condition / control condition, where values <1 were denoted as the negative of its inverse (note that there will be no fold change values between –1 and 1, and that the fold changes of “1” and “-1” represent the same value)
Transcripts were considered significantly differentially expressed using a 10% false discovery rate (DESeq2 adjusted P value < 0.1). Genes were removed from comparisons if they were not expressed above a background threshold (0.5 reads per million) for most samples within each group
Assembly: Rnor_6.0 assembly
Supplementary files format and content: htseq.cov files contain waw counts of reads per gene generated by HTSeq v0.6.1p1.
Supplementary files format and content: AllData_160322_RNASeq_Smoyer_Results_iScience.xlsx contains DESeq2 normalized counts per gene for all samples.
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| Submission date |
Nov 16, 2023 |
| Last update date |
Dec 01, 2024 |
| Contact name |
William E Smoyer |
| E-mail(s) |
[email protected]
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| Organization name |
Nationwide Children's Hospital, Columbus, Ohio
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| Department |
Research
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| Lab |
Smoyer
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| Street address |
700 Children's Dr, Research Building 2
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| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43205 |
| Country |
USA |
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| Platform ID |
GPL22396 |
| Series (1) |
| GSE248053 |
Glucocorticoid- and Pioglitazone-Induced Proteinuria Reduction in Experimental Nephrotic Syndrome Both Correlate with Glomerular ECM Modulation |
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| Relations |
| BioSample |
SAMN38286210 |
| SRA |
SRX22550783 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7905280_116_CONTROL_160217_Dnase.htseq.cov.gz |
135.3 Kb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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