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| Status |
Public on Aug 21, 2018 |
| Title |
Small non-coding RNA expression in developing mouse nephron progenitors |
| Organism |
Mus musculus |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
The overall goal of this study is to determine the small non-coding RNA expression profile in developing mouse nephron progenitors and whole kidney. Using a limited digestion and negative selection approach, an enriched fraction of nephron progenitors were isolated from E15.5 whole kidney samples followed by small RNA-Sequencing (sRNA-Seq). A total of 3 biological replicates of mouse nephron progenitors and whole kidney samples were used for the sRNA-Seq. The NEBNext Multiplex Small RNA Library Prep Kit allowed us to prepare sequencing libraries from as little as 100ng total RNA. Multiplex sequencing was performed using the Illumina NextSeq 550 system with 50bp single reads, resulting in approximately 18 million reads per sample. Reads were aligned to the mm10 genome using Bowtie2, and the miRDeep2 software package was used to identify and quantify known and novel micro RNA (miRNA) within our sRNA-seq libraries. Differential expression analysis of miRNA expression between nephron progenitor and whole kidney samples identified 162 differentially expressed miRNAs (padj <= 0.05).
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| Overall design |
3 biological replicates of nephron progenitors and whole kidney samples were used for the sRNA-Seq. Each replicate consists of material pooled from a single litter of embryos.
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| Contributor(s) |
Phua YL, Clugston A, Chen KH, Ho J, Kostka D |
| Citation(s) |
30422124 |
| Submission date |
Mar 12, 2018 |
| Last update date |
Jan 15, 2019 |
| Contact name |
Andrew Scott Clugston |
| E-mail(s) |
andrew.clugston@pitt.edu
|
| Phone |
4125921754
|
| Organization name |
University of Pittsburgh
|
| Department |
Integrative Systems Biology
|
| Lab |
Ho/Kostka
|
| Street address |
872 Mirror Street
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15217 |
| Country |
USA |
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| Platforms (1) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA437976 |
| SRA |
SRP134975 |
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