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SRX501299: GSM1357180: cntl_neo_5hr_1; Danio rerio; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 32.3M spots, 1.6G bases, 1Gb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Gene expression analysis of hair cell regeneration in the zebrafish lateral line
show Abstracthide Abstract
Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However, non-mammalian animals (e.g. birds, amphibian and fish) regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates, we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA-Seq analyses on regenerating support cells purified by fluorescence activated cell sorting (FACS). The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration, because these cells can be acutely killed by exposure to neomycin, after which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. Tg(sqET20) larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 days post fertilization (dpf) Tg(sqET20) larvae at 1, 3 and 5 hours post neomycin treatment, as well as from a non-treated control. Overall design: Transgenic zebrafish Tg(sqET20) larvae at 5 days post fertilization were exposed to neomycin, dissociated, and FACS sorted into GFP positive and GFP negative populations at 1, 3, and 5 hours following treatment, along with a mock treated 1 hr control. The experiment was performed in triplicate, for a total of 24 samples.
Sample: cntl_neo_5hr_1
SAMN02700065 • SRS582371 • All experiments • All runs
Organism: Danio rerio
Library:
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Two hundred 5dpf untreated Tg(sqET20) control or neomycin treated Tg(sqET20) larvae were anesthetized, collected in a 2mL tube, dissociated with trypsin and filtered to remove un-dissociated tissue. A two-gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions (see Materials and Methods of associated manuscript for detailed FACS protocol). Approximately 30,000 GFP- or GFP+ cells were used for total RNA extraction using Trizol (Invitrogen) following the manufacturer’s manual. Libraries for RNA sequencing were made with poly-A selected mRNA using the Illumina TruSeq RNA library construction kit v2 (Illumina). The resulting libraries were purified using Agencourt AMPure XP system (Backman Coulter), then quantified using a Bioanalyzer or Qubit Fluorometer (Life Technologies).
Experiment attributes:
GEO Accession: GSM1357180
Links:
External link:
Runs: 1 run, 32.3M spots, 1.6G bases, 1Gb
Run# of Spots# of BasesSizePublished
SRR120517232,334,7301.6G1Gb2014-04-01

ID:
691396

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