run_metadata: 42107
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 42107 | SRR5483538 | SRX2766888 | SRS2150990 | 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 | M5 CGATGT L001 R1 001 | M5 | strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateM5L1R1|treatment:MCT8 morpholino|BioSampleModel:Model organism or animal | Pair end L1R1 | M5 CGATGT L001 | M5 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 | M5_CAGATC_L001_R1_001.fastq M5_CAGATC_L001_R2_001.fastq M5_CAGATC_L002_R1_001.fastq M5_CAGATC_L002_R2_001.fastq | fastq fastq fastq fastq | 1042489285.0 | 10734591.0 | M5 CAGATC L002 R1 001.fastq | A:274701145;C:240814745;G:247900443;T:278809711;N:263241 | 274701145 | 240814745 | 247900443 | 278809711 | 263241 | SRX2766888 | SRS2150990 | SRA557338 | Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology | Centro Ciencias do Mar | 2 | 0.93334 | 0.94159 | 0.07462 | 0.07419 | 0.7247 | 0.726 | 0.46897 | 0.47065 | 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 |