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| Status |
Public on Feb 18, 2016 |
| Title |
Metazome_ZF_timecourse_sample_0018 |
| Sample type |
SRA |
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| Source name |
single embryo
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| Organism |
Danio rerio |
| Characteristics |
time (min after fertilization): 720
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
sample_0018
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| 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
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| Submission date |
Aug 21, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Itai Yanai |
| E-mail(s) |
yanai@technion.ac.il
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| Organization name |
Technion - Israel Institute of Technology
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| Department |
Biology
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| Lab |
Yanai
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| Street address |
Technion City
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| City |
Haifa |
| ZIP/Postal code |
30200 |
| Country |
Israel |
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| 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 |
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| Relations |
| BioSample |
SAMN03001910 |
| SRA |
SRX684618 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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