|
| Status |
Public on Aug 11, 2018 |
| Title |
2142_MWF |
| Sample type |
SRA |
| |
|
| Source name |
Munich Wistar Frömter
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: glomerular cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of glomeruli preparations was isolated and DNase-treated by RNeasy Purification Kits (Qiagen)
The NEBNext Poly(A) mRNA magnetic isolation module followed by library preparation using NEBNext Ultra RNA Library Prep Kit for Illumina (New England BioLabs) was applied on 1 µg total RNA to generate a cDNA library
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
MWF Rep3
|
| Data processing |
Basecalls performed using NextSeq 500 RTA software, v. 2.4.6
FASTQ files were generated using bcl2fastq, v.2.16
Raw reads were quality trimmed using Cutadapt v. 1.9 program with the following configurations: minimal base quality: 25, minimal read length after trimming: 70 nt
RNA-seq reads were aligned to the rn6 genome assembly using TopHat2 (v. 2.1.0) and Bowtie2 (v. 2.2.3)
Cufflinks version 2.2.1 program together with Ensembl (release 81) gene annotation were used to assemble transcripts and estimate their abundances
Differential expression analysis was performed using Cuffdiff version 2.2.1 software package and DESeq2 R package version 1.12.4
Genome_build: rn6
Supplementary_files_format_and_content: cuffdiff.gene_exp.diff: gene differential expression produced by Cuffdiff
Supplementary_files_format_and_content: deseq2.results.csv: gene differential expression produced by DeSeq2
|
| |
|
| Submission date |
Aug 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrei Barysenka |
| E-mail(s) |
andrei.barysenka@uni-muenster.de
|
| Organization name |
Institute of Human Genetics, University of Muenster
|
| Department |
Genetic Epidemiology
|
| Street address |
Domagkstrasse 3
|
| City |
Muenster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL20084 |
| Series (1) |
| GSE102546 |
Integrative analysis of the genomic architecture of a complex kidney damage QTL in inbred hypertensive rats implies Tmem63c for translational research |
|
| Relations |
| BioSample |
SAMN07499369 |
| SRA |
SRX3088607 |
