run_metadata: 35952
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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| 35952 | SRR33299157 | SRX28544228 | SRS24843408 | SRP580984 | PRJNA1255065 | A Novel Transgenic Reporter to Study Vertebrate Epigenetics | PRJNA1255065 | Other | Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates. | Het1 ppat liver | strain:ppat|isolate:RNA het1|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal | RNAseq of EpiTag Danio Rerio | RNA het1 | RNA het1 | Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000 | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP580984 | Het1_ppat-liver_S29_R1_001.fastq.gz Het1_ppat-liver_S29_R2_001.fastq.gz | fastq fastq | 8695997521.0 | 43696765.0 | Het1 ppat liver S29 R1 001.fastq.gz | 0:99.39 1:99.62 | A:2300583830;C:2047586482;G:2114382364;T:2227671389;N:5773456 | 99 | 99 | 2300583830 | 2047586482 | 2114382364 | 2227671389 | 5773456 | SRX28544228 | SRS24843408 | SRA2117853 | NIH|NICHD | NIH | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2025-04-24 | Adult | Adult | Liver | Liver and Biliary System |