run_metadata: 42109
This data as json
| rowid | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 42109 | SRR5483536 | SRX2766886 | SRS2150987 | SRP105338 | PRJNA381309 | Danio rerio strain:AB Raw sequence reads | PRJNA381309 | Whole Genome Sequencing | RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf | M7 CGATGT L001 R1 001 | M7 | strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateM7L1R1|treatment:MCT8 morpholino|BioSampleModel:Model organism or animal | Pair end L1R1 | M7 CGATGT L001 | M7 CGATGT L001 | Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures | RNA-Seq | TRANSCRIPTOMIC | RANDOM | PAIRED | ILLUMINA | Illumina HiSeq 1000 | SRP105338 | loader:fastq load.py | M7_GGCTAC_L001_R1_001.fastq M7_GGCTAC_L001_R2_001.fastq M7_GGCTAC_L002_R1_001.fastq M7_GGCTAC_L002_R2_001.fastq | fastq fastq fastq fastq | 1029672796.0 | 10581444.0 | M7 GGCTAC L001 R2 001.fastq | A:272134982;C:235882853;G:243458535;T:277945711;N:250715 | 272134982 | 235882853 | 243458535 | 277945711 | 250715 | SRX2766886 | SRS2150987 | SRA557338 | Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology | Centro Ciencias do Mar | 2 | 0.93095 | 0.93916 | 0.07906 | 0.07917 | 0.72208 | 0.72376 | 0.4638 | 0.47021 | 50 | 50 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | random_priming | trueseq | bulk | unknown | unknown | Portugal | 2017-09-18 | Pharyngula | Embryo | Whole Organism | All anatomical structures |