run_metadata: 11751
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 11751 | ERR11608180 | ERX11010311 | ERS15939665 | ERP148707 | PRJEB63561 | RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors | E-MTAB-13116 | Transcriptome Analysis | Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing. | ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 | Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. | WT2 | E MTAB 13116:WT2 | strain:Tubingen|disease:normal|individual:mixed pool of 200 individuals|organism:Danio rerio|organism:Danio rerio|collection date:not collected|sex:mixed|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|developmental stage:embryo stage|genotype:wild type genotype|isolate:not applicable|immunophenotype:gata1 positive|cell type:erythrocyte|age:48|geographic location country and/or sea:not collected|ENA LAST UPDATE:2023 06 27 | RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors | E MTAB 13116:WT2 p | WT2 p | RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors | The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP148707 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors | ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 | WT2_R1.fastq.gz WT2_R2.fastq.gz | fastq fastq | 8368621500.0 | 27895405.0 | E MTAB 13116:WT2 R | 0:150 1:150 | A:2126734187;C:2050458346;G:2078646608;T:2112586140;N:196219 | 150 | 150 | 2126734187 | 2050458346 | 2078646608 | 2112586140 | 196219 | ERX11010311 | ERS15939665 | ERA24542523 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | 3prime | random_priming | unknown | bulk | unknown | unknown | United Kingdom | 2023-06-27 | Hatching | Embryo | Whole Organism | All anatomical structures |