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Sample GSM1483739 Query DataSets for GSM1483739
Status Public on Feb 18, 2016
Title Metazome_ZF_timecourse_sample_0004
Sample type SRA
 
Source name single embryo
Organism Danio rerio
Characteristics time (min after fertilization): 160
Growth protocol zebrafish fertilization was performed in the lab of Karina Yaniv (Weizmann Institute, Israel). Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. After females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in (REF). Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro-mouthpipette and the embryo flash frozen in liquid nitrogen.
Extracted molecule polyA RNA
Extraction protocol RNA was isolated using TRIzol as previously described (Levin et al., 2012).
The CEL-Seq protocol (Hashimshony, et al. 2012) was used to amplify and sequence. CEL-seq multiplexing barocdes were used.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description sample_0004
Data processing Libraries were sequenced on the Illumina HiSeq2000 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (barcode minimum quality of 10. trimming of read2 to 35 bases - not required).
CEL-Seq (Hashimshony, et a. 2012l) demultiplexing of second mate, using first mate barcode, allowing no mismatches in barcode.
bowtie2, version 2.1.0, against Zv9 genome
Read counting with htseq-count version 0.5.4p3. Using on Ensemble Zv9 annotations
Genome_build: Zv9
Supplementary_files_format_and_content: tabular Expression matrix
 
Submission date Aug 21, 2014
Last update date May 15, 2019
Contact name Itai Yanai
E-mail(s) yanai@technion.ac.il
Organization name Technion - Israel Institute of Technology
Department Biology
Lab Yanai
Street address Technion City
City Haifa
ZIP/Postal code 30200
Country Israel
 
Platform ID GPL14875
Series (2)
GSE60619 Danio rerio high resolution developmental transcriptomic time-course
GSE70185 The mid-developmental transition and the evolution of animal body plans
Relations
BioSample SAMN03001896
SRA SRX684604

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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