run_metadata: 32494

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
32494	SRR29285567	SRX24802697	SRS21518805	SRP511787	PRJNA1120060	O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder	GSE269074	Transcriptome Analysis	Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.		pubmed:39561044		Mutant 5dpf 4	GSM8305914		source name:whole body\|tissue:whole body\|genotype:Mutant\|age:5dpf\|genotype:WT\|replicate:4\|geo loc name:missing\|collection date:missing	Mutant 5dpf 4	FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file	whole body	For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.	Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit	Animals were maintained according to standard protocols	tissue:whole body\|genotype:Mutant\|age:5dpf\|genotype:WT\|replicate:4	GSM8305914	GSM8305914: Mutant 5dpf 4; Danio rerio; RNA Seq	GSM8305914 r1	GSM8305914	1	Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511787			19_S19_R1_001.fastq.gz 19_S19_R2_001.fastq.gz	fastq fastq	5607120194.0	22270005.0	GSM8305914 r1	0:125.80 1:125.98	A:1567782157;C:1175882461;G:1212477800;T:1586827542;N:64150234	125	125			1567782157	1175882461	1212477800	1586827542	64150234	SRX24802697	SRS21518805	SRA1889334	Greenwood Genetic Center	Greenwood Genetic Center	2	0.73788	0.74164	0.26347	0.27285	0.73914	0.74688	0.59711	0.60862	150	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk		United States	2024-06-04	Larval	Larval	Trunk	Surface Structure