run_metadata: 24655

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
24655	SRR25487071	SRX21218616	SRS18475795	SRP452670	PRJNA1000968	CRISPR/Cas9 mediated Nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo	GSE239788	Transcriptome Analysis	Nexilin NEXN plays a crucial role in stabilizing the sarcomeric Z disk of striated muscle fibers and when mutated leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice the detailed impact of the constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated. We characterized a constitutive homozygous CRISPR/Cas9 mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably in contrast to nexn morphants CRISPR/Cas9 nexn / knockout embryos showed a milder phenotype without xxx development of a pronounced pericardial edema or blood congestion. nexn specific expression analysis as well as whole transcriptome profiling suggest some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced and may mediate a sarcomere stabilizing function in nexn / knockout embryos. Overall design: To investigate the influence of nexn knockout on cardiac and skeletal muslce we generated a CRISPR/Cas9 mediated nexn knockout zebrafish model. We then performed gene expression profiling analysis using data obtained from RNA seq.		pubmed:38114601		nexn+/+ biological replicate 1	GSM7673291		source name:whole organism\|tissue:whole organism\|genotype:WT\|geo loc name:missing\|collection date:missing	nexn+/+ biological replicate 1	Raw sequencing data is screened for reads originating from rRNA using RiboDetector eurofins genomics INVIEW transcriptome High quality sequence reads are aligned to the reference genome using STAR Spliced Transcripts Alignment to a Reference run through Sentieon framework along with the known gene models. eurofins genomics INVIEW transcriptome Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool. eurofins genomics INVIEW transcriptome Assembly: GRCz11 Supplementary files format and content: Sample wise gene wise read counts TPM value and FPKM value	whole organism		RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics		tissue:whole organism\|genotype:WT	GSM7673291	GSM7673291: nexn+/+ biological replicate 1; Danio rerio; RNA Seq	GSM7673291 r1	GSM7673291	1	RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP452670		loader:fastq load.py	NG-33220_nexn_E2_sib2_lib693759_10227_2_1.fastq.gz NG-33220_nexn_E2_sib2_lib693759_10227_2_2.fastq.gz	fastq fastq	13610380470.0	45067485.0	GSM7673291 r1	0:151 1:151	A:3776423931;C:3037607848;G:3100752195;T:3694688167;N:908329	151	151			3776423931	3037607848	3100752195	3694688167	908329	SRX21218616	SRS18475795	SRA1684694	Molecular Cardiology, Internal Medicine II, Uniklinik Ulm	Molecular Cardiology, Internal Medicine II, Uniklinik Ulm	2	0.95714	0.95793	0.10127	0.09788	0.69445	0.69278	0.47084	0.46602	151	151	B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	unknown	bulk	bulk	bulk		Germany	2023-08-01	Undetermined	Embryo	Whole Organism	All anatomical structures