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| Status |
Public on Dec 12, 2023 |
| Title |
R00965LF_Control |
| Sample type |
SRA |
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| Source name |
Vestibular ganglion
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Vestibular ganglion
genotype: male Long-Evans
treatment: Control
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| Treatment protocol |
Subchronic ototoxicity rats were given 20 mM of 3,3'-iminodipropionitrile (CAS# 111-94-4; >98%) in the drinking water for 4 weeks; control rats received plain drinking water.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Vestibular ganglia were quickly dissected in ice-cold PBS. Both ganglia from each animal were pooled and stored at -80C. Total RNA was extracted using the Qiagen RNeasy mini kit and protocol.
RNA sequencing libraries were prepared following the SMARTseq2 protocol (Picelli et al., 2014) with some modifications. Briefly, reverse transcription of the total RNA input material of 1.8 µl (6-11 ng, in function of the sample availability) was performed using SuperScript II (Invitrogen) in the presence of oligo-dT30VN (1µM; 5′-AAG CAG TGG TAT CAA CGC AGA GTA CT30VN-3′), template-switching oligonucleotides (1 µM) and betaine (1M). The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (2x) (Roche) and 100 nM IS PCR primer (5′-AAG CAG TGG TAT CAA CGC AGA GT-3′) with 8 cycles of PCR amplification. Following purification with Agencourt Ampure XP beads (1:1 ratio; Beckmann Coulter), the product size distribution and the quantity were assessed with a Bioanalyzer High Sensitivity DNA Kit (Agilent). The amplified cDNA (200 ng) was fragmented for 10 min at 55 ºC using Nextera XT (Illumina) and amplified for 12 cycles with indexed Nextera PCR primers. The library was purified twice with Agencourt Ampure XP beads (0.8:1 ratio) and quantified on a Bioanalyzer using a High Sensitivity DNA Kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
RNAseq reads were mapped to the rat reference genome (Rnor6.0) with STAR/2.5.3a with ENCODE parameters
Genes were quantified with RSEM/1.3.0 with default parameters
The gene annotation file was Rnor6.0.92
Supplementary files format and content: Raw counts (text file)
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| Submission date |
Mar 02, 2023 |
| Last update date |
Dec 12, 2023 |
| Contact name |
Jordi Llorens |
| E-mail(s) |
jllorens@ub.edu
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| Phone |
34934024277
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| Organization name |
Universitat de Barcelona
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| Department |
Ciències Fisiològiques
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| Lab |
4106
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| Street address |
Feixa Llarga s/n
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| City |
Hospitalet de Llobregat |
| State/province |
Catalunya |
| ZIP/Postal code |
08907 |
| Country |
Spain |
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| Platform ID |
GPL14844 |
| Series (2) |
| GSE226516 |
Effect of subchronic ototoxic (3,3'-iminodipropionitrile - IDPN) exposure on the vestibular ganglion of the rat. |
| GSE226517 |
Effect of subchronic ototoxicity on the vestibular ganglion in rodents |
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| Relations |
| BioSample |
SAMN33571805 |
| SRA |
SRX19551571 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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