|
| Status |
Public on Mar 17, 2021 |
| Title |
319 |
| Sample type |
SRA |
| |
|
| Source name |
Renal cortex
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Zucker Diabetic Sprague Dawley
age: 37 weeks
tissue: Renal cortex
experimental group: RYGB surgery
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction from renal cortex was performed using an RNeasy Mini Kit (Qiagen). RNA was isolated according to manufacturer’s instructions. Renal cortical samples were preserved on dry ice prior to lysis steps. RNA samples were stored at -80 degrees Celsius until RNA-sequencing. RNA integrity was checked using a Bioanalyser system prior to sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols. Library preparation kit: TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Quality control of reads performed with fastqc.
Quality filtering of reads performed with trim_galore.
Alignment towards rn5 rat reference genome using STAR.
Quantification of aligned reads using featureCounts (Subread package).
Differential expression analysis using DESeq2.
Genome_build: rn5 (Rnor_5.0) rat reference genome
Supplementary_files_format_and_content: *_featureCounts.txt: Tab-delimited text files providing raw counts of aligned reads for each rat renal cortical sample.
|
| |
|
| Submission date |
Mar 29, 2020 |
| Last update date |
Mar 17, 2021 |
| Contact name |
William P. Martin |
| E-mail(s) |
liampvmartin1992@gmail.com, william.martin@ucd.ie
|
| Organization name |
University College Dublin
|
| Street address |
Diabetes Complications Research Centre, Conway Institute, University College Dublin
|
| City |
Dublin |
| State/province |
- Select State/Province - |
| ZIP/Postal code |
Dublin 4 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE147706 |
RNA-Sequencing Characterisation of the Renal Cortical Response to Roux-en-Y Gastric Bypass Surgery Alone and Combined Roux-en-Y Gastric Bypass Surgery and Medical Therapy in the Zucker Diabetic Sprague Dawley Rat Model of Diabetic Kidney Disease |
|
| Relations |
| BioSample |
SAMN14483225 |
| SRA |
SRX8023361 |
