|
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 |