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| Status |
Public on Apr 30, 2013 |
| Title |
Prim-25, 36hpf |
| Sample type |
SRA |
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| Source name |
Zebrafish embryos at the Prim-25 stage
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| Organism |
Danio rerio |
| Characteristics |
strain: AB
developmental stage: Prim-25, 36hpf
tissue: embryo
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| Treatment protocol |
Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.
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| Growth protocol |
Zebrafish embryos and larvae were collected and maintained at approximately 28.5°C, and were staged according to their morphological features and hours (h) or days (d) post-fertilization as described previously (Kimmel et al. 1995)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from each stage of (about 2000) embryos or larvae using Trizol (Invitrogen,Carlsbad, CA, USA) methods according to the manufacturer’s instruction. RNA quality was evaluated by gel electrophoresis, and the concentration was measured with NanoDrop 2000 (Thermo Scientific，Waltham, MA,USA).The aliquots were stored at -80 oC.
A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA-seq libraries. First, the total RNA was estimated on an Agilent 2100 Bioanalyzer (Agilent Technologies,Waldbronn,Germany). Second, The ribosomal RNA-removal steps were replaced by two rounds of polyA purification, with the first round using the PolyATtract® mRNA Isolation Systems (Promega, Madison, WI, USA) and the second round using the Poly(A)Purist™ Kit (Ambion, Austin, TX, USA). About 0.8 μg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A, subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE-Urea Gel (Invitrogen, Carlsbad, CA, USA) and 100–200 nt fraction was recovered. The fractionated cDNA were subjected to 11-15 cycles of PCR amplification, with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 3.0 |
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| Description |
~2000 individuals
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| Data processing |
Primary processing by SOLiD 3.0 online software
The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope (v1.2) obtained from Life Techlogies.
Reads per kilobase of transcript per million mapped reads (RPKM) were calculated using an in-house developed perl script, which is available upon request.
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for gene models from the genome annotation ((release Ensembl 62) of the Zv9 assembly
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| Submission date |
Apr 02, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Hongxing Yang |
| E-mail(s) |
yanghx81@gmail.com
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| Organization name |
Shanghai Chenshan Botanical Garden
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| Street address |
3888 Chenhua Rd, Songjiang District
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| City |
Shanghai |
| State/province |
- |
| ZIP/Postal code |
201602 |
| Country |
China |
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| Platform ID |
GPL10658 |
| Series (1) |
| GSE45706 |
RNA-sequencing project for zebrafish embryo and larva development |
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| Relations |
| SRA |
SRX258164 |
| BioSample |
SAMN01996037 |
| 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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