run_metadata: 72794
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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| 72794 | SRR23149200 | SRX19099970 | SRS16514932 | SRP418428 | PRJNA925841 | The function and mechanism of aldh9a1b in diabetes | GSE223340 | Transcriptome Analysis | Reactive aldehydes such as 4 HNE MDA and acrolein are implicated in the pathological development of diabetes as their widespread and universally exposed characteristics. Trans trans 2 4 decadienal tt DDE come from lipid peroxidation of omega 6 and is most abundant aldehyde in cooking oil fumes while its role in diabetes remained unknown. Aldh9a1 is a cytosolic enzyme that catalyze the NAD+ dependent oxidation of a variety of aldehydes and has its homology aldh9a1b in zebrafish. To investigate the function of endogenous and exogenous tt DDE aldh9a1b knockout zebrafish are established using CRISPR/Cas9 technology. TT DDE was confirmed to act as substrate for aldh9a1b and a series of experiments are performed on a histological metabolomic and transcriptomic level in aldh9a1b / zebrafish. Both aldh9a1b / larvae and adult fish displayed abnormal retinal vasculature and impaired glucose homeostasis which are caused by tt DDE induced downregulated insulin signaling pathway. Furthermore the abnormal hyaloid vasculature in the fish can be reversed by insulin receptor sensitizer and metformin exhibited strongest effects among them. Altogether these results identified tt DDE as the preferred substrate for aldh9a1b which subsequently causes microvascular damage and impaired glucose metabolism by insulin resistance. Overall design: A CRISPR based knockout ofaldh9a1b was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on the larvae of aldh9a1b+/+ aldh9a1b / and tt DDE treating aldh9a1b+/+ by BGI . | pubmed:38059818 | ALDH9A1B +/+ 1 | GSM6945826 | source name:Tgfli1:EGFP|tissue:larvae|treatment:no|genotype:WT|geo loc name:missing|collection date:missing | ALDH9A1B +/+ 1 | QC with fastqc nersion 0.11.9 Parameters:fastqc *.fastq trimmed with trim galore version 0.6.7. Parameters: trim galore phred33 q 30 length 36 stringency 3 alignment with hisat2 version 2.2.1 . Parameters: hisat2 t p 30 x Get raw counts with featureCounts Version 2.0.1. Parameters: featureCounts T 5 p t exon g gene id a Assembly: GRCz11 Supplementary files format and content: Raw counts generated with featureCounts Version 2.0.1. | Tgfli1:EGFP | Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|treatment:no|genotype:WT | GSM6945826 | GSM6945826: ALDH9A1B +/+ 1; Danio rerio; RNA Seq | GSM6945826 r1 | GSM6945826 | 1 | Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP418428 | 9a1b_wt1_1.fq.gz 9a1b_wt1_2.fq.gz | fastq fastq | 4815315800.0 | 48153158.0 | GSM6945826 r1 | 0:100 1:100 | A:1247999014;C:1152843910;G:1160913120;T:1253559756;N:0 | 100 | 100 | 1247999014 | 1152843910 | 1160913120 | 1253559756 | 0 | SRX19099970 | SRS16514932 | SRA1577387 | Vascular Biology&Tumor Angiogenesis, Medical Faculty Mannheim, Heidelberg University | Vascular Biology&Tumor Angiogenesis, Medical Faculty Mannheim, Heidelberg University | 1 | 0.96307 | 0.07602 | 0.65949 | 0.46055 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2023-01-20 | Larval | Larval | Undetermined | Undetermined |