|
| Status |
Public on Dec 31, 2018 |
| Title |
Heat Shock 2 |
| Sample type |
SRA |
| |
|
| Source name |
Adult mouse utricle explant
|
| Organism |
Mus musculus |
| Characteristics |
strain: CBA/J
tissue: Vestibular system tissue (Utricle)
age: Adult (P30-P60)
treatment: Heat Shock
classification: Cultured
|
| Treatment protocol |
Following overnight culture, utricles were transferred into a sterile microcentrifuge tube using a sterile glass pipette. The centrifuge tube was transferred into a water bath held at 43C for 30 minutes to induce a heat shock response. Following this induction, utricles were returned to 37C and recovered for 2 hours to up-regulate the transcriptional heat shock response
|
| Growth protocol |
Adult CBA/J mice (male and female) were anesthetized, decapitated, and temporal bones were dissected out into M199 media (Life Technologies). Utricles were dissected using sterile forceps in a tissue culture hood, and were transferred into sterile 24-well plates (Life Technologies). The utricles were cultured overnight at 37C and 95% air/5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Disruption and homogenization of tissues was performed by triturating tissue in lysis buffer with a sterile 27G syringe, and extraction of RNA was accomplished using the RNAqueous micro kit protocol (Ambion).
SMARTer Ultra Low RNA kit (Clontech) was used to prepare double-stranded cDNA. Nextera XT (Illumina) was used for library preparation
Double-stranded cDNA library, paired end sequencing, multiplexed libraries
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Whole Tissue
HS-2_S6
|
| Data processing |
FastQC and Trimmomatic
STAR Alignment to GRCm38
featureCounts (subread) to generate raw gene counts
Differential gene expression using DESeq2, EdgeR, Limma Voom
Genome_build: GRCm38.p3 Release M4
|
| |
|
| Submission date |
Jul 02, 2018 |
| Last update date |
Nov 21, 2022 |
| Contact name |
Robert Morell |
| E-mail(s) |
morellr@nidcd.nih.gov
|
| Organization name |
National Institute on Deafness and Other Communication Disorders
|
| Street address |
35A Convent Drive, Room 1F-103
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE116515 |
The inner ear heat shock transcriptional signature identifies otoprotective compounds against aminoglycoside ototoxicity |
|
| Relations |
| BioSample |
SAMN09534081 |
| SRA |
SRX4333342 |
