run_metadata: 60554

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
60554	SRR12354655	SRX8854017	SRS7115701	SRP274361	PRJNA649779	Unveiling the role of RAB13 localisation in angiogenesis	GSE155449	Other	Deciphering the complex biology of cell migration is key to understand human related disorders. During angiogenesis endothelial cells engage in coordinated migration events to form new blood vessels from parental counterparts. However while subcellular localisation of mRNAs and localised translation are fundamental steps between gene transcription and protein activity whether local regulation of gene expression controls the complex morphogenetic process of angiogenesis has never been addressed. Here we focused on RAB13 mRNA a transcript enriched at the leading front of many migratory cell types. We set out to delete regions in the three primeUTR of RAB13 mRNA responsible for its subcellular distribution in vitro and in vivo and to study its localised role during angiogenesis. Overall design: post identifying regions responsible for the localisation of RAB13 mRNA we used CRISPR/Cas9 technology with gRNAs targeting the three primeUTR of both human and zebrafish orthologues. We performed RNA seq experiments using RNA derived from control and mutant samples to 1 investigate whether potential off target sites were edited by CRISPR/Cas9 and 2 analyse the expression of potential RAB13 splicing variants. Samples analysed: HUVECs 1x Wild type and 1x Homozygous RAB13 three primeUTR; Zebrafish 2x Wild type and 2x Homozygous RAB13 three primeUTR. Description of RAB13 three primeUTR mutations: Deletion of 190 nucleotides from Human RAB13 three primeUTR Deletion of 482 nucleotides from Zebrafish RAB13 three primeUTR		pubmed:32946121		WT Zebrafish 1	GSM4704580		source name:Zebrafish embryo\|tissue:28 hpf embryo trunk\|genotype:Wild type\|passage:N/A	WT Zebrafish 1	The stranded paired end RNA seq reads were quality assessed using FastQC v0.11.3 and FastQ Screen v0.9.2. The raw reads were processed with BBDuk part of the BBMap suite; v36.32 to trim the adapter sequences and low quality bases. Processed reads from the human derived samples were mapped against the reference assembly hg38 using STAR v2.7.2b with “–quantMode GeneCounts” option to obtain read count for each gene annotated in GENCODE v32 whereas reads from the zebrafish derived samples were mapped against the reference assembly GRCz11 and gene annotation from Ensembl v99. Genome build: hg38 HUVEC samples; GRCz11 zebrafish samples Supplementary files format and content: bigWig files include RPKM values for each sample	Zebrafish embryo	HUVECs – cells were transfected with sgRNA Cas9 ribonucleoproteins and a GFP expressing plasmid. GFP+ cells were harvested 48 hours later and single cell FACS sorted in 96 well plates. post amplification cells were PCR genotyped and RNA was extracted from 1 non edited exemplar clone WT and 1 exemplar clone with bi allelic targeted deletion.	Zebrafish – zygote stage embryos were injected with sgRNA Cas9 ribonucleoproteins and grown to adult stages. Germline transmission of targeted deletion was performed by PCR and 1 desired founder animal F0 was identified. The F0 was outcrossed to Wt animals to generate F1 heterozygous animals. F1 animals were incrossed and the resulting offspring was grown 28 hours stage embryos. Heads were dissected for PCR genotyping and the trunks of 2 WT and 2 HOM embryos were processed for RNA extraction. RNA seq library prepared with TruSeq Stranded mRNA Illumina	HUVECs were cultured in complete ECGM2 in gelatin coated dishes. Zebrafish were maintained and bred according to standard conditions.	tissue:28 hpf embryo trunk\|genotype:Wild type\|passage:N/A	GSM4704580	GSM4704580: WT Zebrafish 1; Danio rerio; RNA Seq	GSM4704580		1	Zebrafish – zygote stage embryos were injected with sgRNA Cas9 ribonucleoproteins and grown to adult stages. Germline transmission of targeted deletion was performed by PCR and 1 desired founder animal F0 was identified. The F0 was outcrossed to Wt animals to generate F1 heterozygous animals. F1 animals were incrossed and the resulting offspring was grown 28 hours stage embryos. Heads were dissected for PCR genotyping and the trunks of 2 WT and 2 HOM embryos were processed for RNA extraction. RNA seq library prepared with TruSeq Stranded mRNA Illumina	GEO Accession:GSM4704580	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP274361			WT1_ZFISH_R1_001.fastq.gz WT1_ZFISH_R2_001.fastq.gz	fastq fastq	8044011744.0	54777035.0	GSM4704580 r1	0:73.46 1:73.39	A:2032870189;C:1897481528;G:1840068049;T:2099766774;N:173825204	73	73			2032870189	1897481528	1840068049	2099766774	173825204	SRX8854017	SRS7115701	SRA1105789	GEO	University of Manchester	2	0.94397	0.93722	0.0896	0.08658	0.70713	0.70871	0.46726	0.47109	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown		United Kingdom	2020-07-30	Multi-stage	Embryo	Trunk	Surface Structure