|
| Status |
Public on Nov 12, 2018 |
| Title |
K002000053_48003 |
| Sample type |
SRA |
| |
|
| Source name |
intraperitoneal cisplatin (cis)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: kidney
age: 20 weeks
preconditioning: baseline
injection: intraperitoneal cisplatin (cis)
|
| Treatment protocol |
treatment: organ harvest 72 h hours after intraperitoneal cisplatin (cis) or vehicle (sodium chloride 0.9%, veh) injection. HP: preconditioning of the mice by hypoxia (2 h, 4 h, 8 h) on three following days at least 1 h prior to injection CR: preconditioning of the mice by calorie restriction 4 weeks prior to injection BL: no preconditioning of the mice prior to injection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All animals were perfused with phosphate buffered saline and kidneys were extracted immediately afterwards. Then they were divided into to halves and immediately put into liquid nitrogen. Afterwards they were stored at -80°C. until RNA preparation. From 1 µl input of total RNA, ribosomal RNA was removed using biotinylated target-specific oligos combined with Ribo-Zero rRNA removal beads. Samples of cytoplasmic rRNA wer depleted by the Ribo-Zero Human/Mouse/Rat kit. RNA was fragmented into small pieces using divalent cations under elevated temperature. After copying the cleaved RNA fragments into first strand cDNA using random primers and reverse transcriptase, the second strand cDNA synthesis was performed with DNA DNA Polymerase I and RNase H. Then single‘A’ base was added and subsequently adapter ligation took place.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-seq total RNA – rRNA depleted by the Ribo-Zero Human/Mouse/Rat kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Paired end total RNA-seq data was mapped to the mouse genome (mm10) using STAR aligner (v.2.5) with the default options and splice junction annotation from Ensembl (GRCm38.83).
Count value for each gene was obtained using featureCount command from subread program (v.1.5) with the following options: paired end (-p) only considering primary alignment (--primary) and strand-specific for reverse forward protocol (-s 2; -S fr).
For normalization, we used the transcript per millions (TPM).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM for each sample.
|
| |
|
| Submission date |
Nov 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Andreas Beyer |
| Organization name |
University of Cologne
|
| Department |
System Biology
|
| Lab |
Beyer lab
|
| Street address |
Joseph-Stelzmann-Str. 26
|
| City |
Cologne |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE106993 |
Transcriptomic dataset after cisplatin induced acute kidney injury |
|
| Relations |
| BioSample |
SAMN08032739 |
| SRA |
SRX3398938 |
