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Sample GSM1357170 Query DataSets for GSM1357170
Status Public on Mar 26, 2014
Title gfp_nt_1hr_3
Sample type SRA
 
Source name GFP positive cells from 5 dpf larvae
Organism Danio rerio
Characteristics drug: no drug
time: 1hr
gfp status: positive
genotype: Tg(sqET20)
experiment_date: Mar2012
Treatment protocol For neomycin treatment, 5dpf larvae were treated for 30min with 300μM neomycin (Fisher BioReagents) diluted in 0.5X E2 medium, rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.
Growth protocol Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild-type larvae at 48 hpf under fluorescent stereoscope.
Extracted molecule total RNA
Extraction 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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Data was processed with CASAVA version 1.8.2
Sequence reads in fastq format were mapped to danRer7using tophat-1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3.
Genome_build: danRer7
Supplementary_files_format_and_content: FPKM values per gene.
 
Submission date Mar 25, 2014
Last update date May 15, 2019
Contact name Chris W Seidel
E-mail(s) seidel@phageT4.org
Phone 816 926 9054
Organization name Stowers Institute
Department Genomics
Lab Seidel
Street address 1000 E 50th St
City Kansas City
State/province MO
ZIP/Postal code 64110
Country USA
 
Platform ID GPL14875
Series (1)
GSE56176 Gene expression analysis of hair cell regeneration in the zebrafish lateral line
Relations
BioSample SAMN02700067
SRA SRX501289

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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