run_metadata: 75097

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
75097	SRR24239722	SRX20035837	SRS17374852	SRP433739	PRJNA958104	The secreted neuronal signal Spock1 regulates the blood brain barrier	GSE230236	Transcriptome Analysis	The blood brain barrier BBB is a unique set of properties of the brain vasculature which severely restricts its permeability to proteins and small molecules. Classic chick quail chimera studies showed that these properties are not intrinsic to the brain vasculature but rather are induced by surrounding neural tissue. Here we identify Spock1 as a candidate neuronal signal for regulating BBB permeability in zebrafish and mice. Mosaic genetic analysis shows that neuronally expressed Spock1 is cell non autonomously required for a functional BBB. Leakage in spock1 mutants is associated with altered extracellular matrix ECM increased endothelial transcytosis and altered pericyte endothelial interactions. Furthermore a single dose of recombinant SPOCK1 into spock1 mutants quenches gelatinase activity restores vascular expression of BBB genes including mcamb and partially restores barrier function. These analyses support a model in which neuronally secreted Spock1 induces BBB properties by altering the ECM thereby regulating pericyte endothelial interactions and downstream vascular gene expression. Overall design: Bulk RNAseq Libraries 66 71 of leaky mutant and wild type siblings to identify the genetic lesion responsible for the leaky phenotype. These analyses revealed linkage to chr14 and more specifically to the spock1 gene. scRNAseq Library scDRBrain of dissected spock1 mutant and wild type brains was then used to identify all cell type specific changes in gene expression in the mutant background.		pubmed:37437574		pooled wild type heads 5dpf [WT 67]	GSM7208215		tissue:mixed\|cell type:mixed\|genotype:WT\|time:5 dpf\|geo loc name:missing\|collection date:missing	pooled wild type heads 5dpf [WT 67]	CLC Genomics Workbench v 11.0.1 Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchwork parameter Quality limit: 0.05 Trimmed sequence reads were mapped to GRCz11 using tophat and bowtie2 with default parameters. Read counts were generated using rsem Assembly: GRCz11 Supplementary files format and content: The gene counts matrix is an output from rsem differential gene expression analysis and is a raw counts estimate not normalized for each gene. The first column is gene name and then post that each column represents an individual sample WT for the first 3 and then MUT for the last 3. Supplementary files format and content: The h5ad file contains the counts matrix for the demultiplexed single cell data. This file also holds relevant genotype and timepoint annotations as well as Multi seq barcode counts for each cell.	mixed		RNA was harvested using Rneasy mini plus kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using Wafergen Directional RNA Seq Library Prep Kit following manufacturer's protocols.		cell type:mixed\|genotype:WT\|time:5 dpf	GSM7208215	GSM7208215: pooled wild type heads 5dpf [WT 67]; Danio rerio; RNA Seq	GSM7208215 r1	GSM7208215	1	RNA was harvested using Rneasy mini plus kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using Wafergen Directional RNA Seq Library Prep Kit following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP433739			WT_67_1.fastq.gz WT_67_2.fastq.gz	fastq fastq	4212400800.0	28082672.0	GSM7208215 r1	0:75 1:75	A:1024709764;C:1090887683;G:1098819017;T:997964994;N:19342	75	75			1024709764	1090887683	1098819017	997964994	19342	SRX20035837	SRS17374852	SRA1728506	Megason Lab, Systems Biology, Harvard Medical School	Megason Lab, Systems Biology, Harvard Medical School	2	0.99585	0.99873	0.27061	0.26987	0.9274	0.92801	0.66832	0.75671	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk		United States	2023-04-21	Larval	Larval	Head	Nervous System