run_metadata: 10660
This data as json
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| 10660 | ERR406892 | ERX373251 | ERS391750 | ERP004564 | PRJEB5188 | YD embryos 8 hpf 24 hpf 32 hpf | E-MTAB-2194 | Transcriptome Analysis | Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq. | Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 | 6y32 | SAMEA2299292 | CAS-MPG PICB | ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:37Z|External Id:SAMEA2299292|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:37Z|INSDC status:public|Submitter Id:E MTAB 2194:6y32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6y32|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb | Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf | E MTAB 2194:Unique sample ID.11 | batchB 32hpf YD | YD embryos 8 hpf 24 hpf 32 hpf | Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 | Experimental Factor: treatment:yolk|Experimental Factor: time:32 hour | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | ERP004564 | Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf | ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16 | 6y32.fq.gz | fastq | 568482400.0 | 11369648.0 | E MTAB 2194:6y32.fq.gz | 0:50 1:0 | A:149679881;C:135411801;G:134312216;T:149069222;N:9280 | 50 | 0 | 149679881 | 135411801 | 134312216 | 149069222 | 9280 | ERX373251 | ERS391750 | ERA280282 | CAS-MPG PICB|ArrayExpress | CAS-MPG PICB|ArrayExpress | 1 | 0.93184 | 0.104 | 0.68128 | 0.47652 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | random_priming | trueseq | bulk | unknown | unknown | China | 2014-04-01 | Multi-stage | Embryo | Whole Organism | All anatomical structures |