run_metadata: 55355
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 |
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| 55355 | SRR10312403 | SRX7023623 | SRS5544399 | SRP226227 | PRJNA578399 | RNA seq of etv2 mutant knock in heterozygous and homozygous zebrafish embryos | GSE139108 | Transcriptome Analysis | Zebrafish etv2^Gt2A Gal4ci32 line was generated using CRISPR Cas9 mediated NHEJ approach which has 2A Gal4 sequence inserted with the exon 5 of etv2 gene thus interrupting etv2 coding sequence. Heterozygous and homozogous embryos were subjected to bulk RNA seq Overall design: 3 batches of 15 20 heterozygous and homozygous embryos were frozen at the 15 somite and 24 hpf stages. Total 12 samples were sequenced: triplicate samples of Heterozygous and homozygous embryos at 15 somite and 24 hpf stages | pubmed:31705559 | etv2 het 15som 2 | GSM4131103 | source name:Whole embryos|tissue:Whole embryos|line allele:etv2^Gt2A Gal4ci32|genotype:Heterozygous|embryo stage:15 somite | etv2 het 15som 2 | Sequencing was performed at 20M PE 150 read depth by Novogene Inc Alignment to the zebrafish genome was performed using Strand 3.0 software using default parameters. Genome build: Zv9 Supplementary files format and content: Excel files include triplicate samples from heterozygous or homozygous embryos at each stage. DESeq normalized log scaled RPKM values are provided | Whole embryos | 3 batches of heterozygous and homozygous embryos 15 20 embryos each were sorted based on GFP expression pattern and frozen on dry ice. | Bulk RNA was purified using RNA quous 4 PCR kit ThermoFisher. Library synthesis was performed using NEB Next Ultra RNA library Prep Kit by Novogene Inc | etv2^ci32Gt heterozygous and homozygous embryos were obtained from the incross of etv2^ci32Gt+/ ; UAS:GFP carriers. Embryos were incubated at 28 C for 24 hpf stage and at 24 C for 15 somite stage. | tissue:Whole embryos|line allele:etv2^Gt2A Gal4ci32|genotype:Heterozygous|embryo stage:15 somite | GSM4131103 | GSM4131103: etv2 het 15som 2; Danio rerio; RNA Seq | GSM4131103 | 1 | Bulk RNA was purified using RNA quous 4 PCR kit ThermoFisher. Library synthesis was performed using NEB Next Ultra RNA library Prep Kit by Novogene Inc | GEO Accession:GSM4131103 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP226227 | Gal4_S_15som_2_2.fq.gz Gal4_S_15som_2_1.fq.gz | fastq fastq | 6470013600.0 | 21566712.0 | GSM4131103 r1 | 0:150 1:150 | A:1776945744;C:1463614010;G:1487591153;T:1740908499;N:954194 | 150 | 150 | 1776945744 | 1463614010 | 1487591153 | 1740908499 | 954194 | SRX7023623 | SRS5544399 | SRA982009 | GEO | Division of Developmental Biology, Cincinnati Children's Hospital Medical Center | 2 | 0.9287 | 0.92958 | 0.09528 | 0.09614 | 0.71735 | 0.73265 | 0.48939 | 0.47903 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | nebnext | bulk | bulk | bulk | United States | 2019-10-18 | Segmentation | Embryo | Whole Organism | All anatomical structures |