run_metadata: 10665
This data as json
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| 10665 | ERR406884 | ERX373246 | ERS391745 | 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 Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 | 6s32 | SAMEA2299287 | CAS-MPG PICB | ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:26Z|External Id:SAMEA2299287|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:26Z|INSDC status:public|Submitter Id:E MTAB 2194:6s32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6s32|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.12 | batchB 32hpf SP | YD embryos 8 hpf 24 hpf 32 hpf | Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2 | Experimental Factor: treatment:sham punctured embryos|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 | 6s32.fq.gz | fastq | 652353200.0 | 13047064.0 | E MTAB 2194:6s32.fq.gz | 0:50 1:0 | A:170844587;C:156203331;G:155264927;T:170029850;N:10505 | 50 | 0 | 170844587 | 156203331 | 155264927 | 170029850 | 10505 | ERX373246 | ERS391745 | ERA280282 | CAS-MPG PICB|ArrayExpress | CAS-MPG PICB|ArrayExpress | 1 | 0.93785 | 0.09102 | 0.68554 | 0.46397 | 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 |