NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1029655 Query DataSets for GSM1029655
Status Public on Sep 19, 2013
Title FliRas 3df
Sample type SRA
 
Source name Whole zebrafish larvae
Organism Danio rerio
Characteristics Stage: 3 days post fertilization
tissue: whole larvae
genetic background: AB
genotype: (Tg(fli1ep:GAL4FF)ubs3; Tg(UAS:eGFP-HRASV12)io006
Growth protocol Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).
Extracted molecule total RNA
Extraction protocol Larvae for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 10 ug of total RNA for the construction of sequencing libraries.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Base-calls and demultiplexing using Illumina Casava 1.8.
Low-quality base-calls were removed using the 'quality_trim' application in the CLC bio Assembly Cell 3.2 software package. Settings: minimum remaining read length 30, minimum quality 20, at least 50% of the read must be good quality.
Reads were aligned to Ensembl predicted cDNAs (Danio_rerio.Zv9.63.cdna.all.fa) using the 'clc_ref_assemble_short' application in the CLC bio Assembly Cell 3.2 software package. Settings: mismatch cost 2, gap cost 3, deletion cost 3, score limit 8; random placement of repeats, up to 50 alignments per read.
Alignment files were translated into counts per transcript using the 'assembly_table' application, and summarized into genes based on Ensembl transcript/gene annotations using a custom script. Non-unique alignments were divided amongst target genes by ratio of unique reads, yielding a corrected total reads count per gene. This count was divided by the total length of constituent transcripts and by the total number of aligned read, and multiplied by a billion, to arrive at a RPKM-like expression value.
Genome_build: Zv9 (Ensembl release 63)
Supplementary_files_format_and_content: Tab-delimited text files with read counts and RPKM-normalized values for every gene.
 
Submission date Nov 01, 2012
Last update date May 15, 2019
Contact name marina mione
E-mail(s) maria.mione@kit.edu
Organization name Karlsruhe Institute of Technology
Department Institute of Toxicology and Genomics
Street address Hermann-von-Helmholtz-Platz 1
City Eggesteing Leopolshafen
ZIP/Postal code 76344
Country Germany
 
Platform ID GPL14875
Series (1)
GSE41988 Targeting oncogene expression to endothelial cells induces proliferation of the myelo-erythroid lineage by repressing the notch pathway
Relations
BioSample SAMN01797980
SRA SRX202491

Supplementary file Size Download File type/resource
GSM1029655_FliRAS3dpf_genes.txt.gz 411.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap