run_metadata: 67044
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 67044 | SRR17017806 | SRX13207903 | SRS11133998 | SRP347444 | PRJNA782975 | Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis | GSE189416 | Transcriptome Analysis | In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health. | pubmed:35114580 | Aldh 2.1 / KO la2 | GSM5701221 | source name:whole larvae|developmental stage:larvae 120hpf|tissue:whole larvae|genotype:aldh2.1 knockout | Aldh 2.1 / KO la2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | whole larvae | Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment. | developmental stage:larvae 120hpf|tissue:whole larvae|genotype:aldh2.1 knockout | GSM5701221 | GSM5701221: Aldh 2.1 / KO la2; Danio rerio; RNA Seq | GSM5701221 r1 | GSM5701221 | 1 | Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP347444 | 2-KOla2_1.fq.gz 2-KOla2_2.fq.gz | fastq fastq | 4993502200.0 | 49935022.0 | GSM5701221 r1 | 0:100 1:100 | A:1337290403;C:1130744731;G:1181303599;T:1344163467;N:0 | 100 | 100 | 1337290403 | 1130744731 | 1181303599 | 1344163467 | 0 | SRX13207903 | SRS11133998 | SRA1492011 | ZMF, University Heidelberg | ZMF, University Heidelberg | 1 | 0.95056 | 0.09273 | 0.69207 | 0.5213 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-11-23 | Larval | Larval | Whole Organism | All anatomical structures |