run_metadata: 11227

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
11227	ERR10368638	ERX9900561	ERS13563107	ERP141667	PRJEB56699	RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70	E-MTAB-12301	Other	It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced.	ENA FIRST PUBLIC:2022 10 31\|ENA LAST UPDATE:2022 10 31		Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold	16261X8	SAMEA111469071	Department of Life Sciences University of Bath	ENA FIRST PUBLIC:2022 10 31\|ENA LAST UPDATE:2022 10 31\|External Id:SAMEA111469071\|INSDC center alias:Department of Life Sciences University of Bath\|INSDC center name:Department of Life Sciences University of Bath\|INSDC first public:2022 10 31T00:16:52Z\|INSDC last update:2022 10 31T00:16:52Z\|INSDC status:public\|Submitter Id:E MTAB 12301:16261X8\|age:28\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|disease:normal\|genotype:snrnp70 / \|organism part:whole organism\|sample name:E MTAB 12301:16261X8									Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70	E MTAB 12301:16261X8 p	16261X8 p	RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70	Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold	Experimental Factor: genotype:snrnp70 /	RNA-Seq	TRANSCRIPTOMIC	Inverse rRNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP141667	Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70	ENA FIRST PUBLIC:2022 10 31\|ENA LAST UPDATE:2022 10 31	16261X8_190815_A00421_0101_BHFL23DRXX_S4_L001_R1_001.fastq.gz 16261X8_190815_A00421_0101_BHFL23DRXX_S4_L001_R2_001.fastq.gz	fastq fastq	15003930006.0	147097353.0	E MTAB 12301:16261X8 190815 A00421 0101 BHFL23DRXX S4 L001 R	0:51 1:51	A:3882939949;C:3570150556;G:3520942177;T:4028462946;N:1434378	51	51			3882939949	3570150556	3520942177	4028462946	1434378	ERX9900561	ERS13563107	ERA18523376	Department of Life Sciences University of Bath\|European Nucleotide Archive	Department of Life Sciences University of Bath\|European Nucleotide Archive	2	0.94373	0.94762	0.17954	0.17832	0.70299	0.70207	0.48822	0.48842	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	rrna_depletion	trueseq	bulk	bulk	bulk		United Kingdom	2022-10-31	Pharyngula	Embryo	Whole Organism	All anatomical structures