run_metadata: 74916

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
74916	SRR24149998	SRX19948131	SRS17296333	SRP432326	PRJNA954890	RhoA GEF Mcf2lb regulates rosette integrity during collective cell migration	GSE229567	Other	During development multicellular rosettes serve as important cellular intermediates in the formation of diverse organ systems. Multicellular rosettes are transient epithelial structures that are defined by the apical constriction of cells towards the rosette center. Due to the important role these structures play during development understanding the molecular mechanisms by which rosettes are formed and maintained is of high interest. Utilizing the zebrafish posterior lateral line primordium pLLP as a model system we identify the RhoA GEF Mcf2lb as a regulator of rosette integrity. The pLLP is a group of 150 cells that migrates along the zebrafish trunk and is organized into epithelial rosettes; these are deposited along the trunk and will differentiate into sensory organs called neuromasts NMs. Using single cell RNA sequencing and whole mount in situ hybridization we showed that mcf2lb is expressed in the pLLP during migration. Given the known role of RhoA in rosette formation we asked whether Mcf2lb plays a role in regulating apical constriction of cells within rosettes. Live imaging and subsequent 3D analysis of mcf2lb mutant pLLP cells showed disrupted apical constriction and subsequent rosette organization. This in turn resulted in a unique posterior Lateral Line phenotype: an excess number of deposited NMs along the trunk of the zebrafish. Cell polarity markers ZO 1 and Par 3 were apically localized indicating that pLLP cells are normally polarized. In contrast signaling components that mediate apical constriction downstream of RhoA Rock 2a and non muscle Myosin II were diminished apically. Altogether our results suggest a model whereby Mcf2lb activates RhoA which in turn activates downstream signaling machinery to induce and maintain apical constriction in cells incorporated into rosettes. Overall design: Cells from Tg 8.0claudinB: lynGFPzf106; TgBACcxcr4b:F tractin mCherry transgenic line were isolated by Fluorescence activated cell sorting FACS according to the presence or absence of GFP and mCherry signal and analyzed using scRNAseq.		pubmed:37131612;pubmed:38165177		Tg 8.0claudinB: lynGFPzf106; TgBACcxcr4b:F tractin mCherry transgenic line scRNAseq	GSM7165622		source name:zebrafish embryo\|cell type:various\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf	Tg 8.0claudinB: lynGFPzf106; TgBACcxcr4b:F tractin mCherry transgenic line scRNAseq	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		30 hpf Tg 8.0claudinB:lynGFPzf106/ TgBACcxcr4b:F tractin mCherry zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube Library was performed according to the manufacturer’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:various\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf	GSM7165622	GSM7165622: Tg 8.0claudinB: lynGFPzf106; TgBACcxcr4b:F tractin mCherry transgenic line scRNAseq; Danio rerio; RNA Seq	GSM7165622 r1	GSM7165622	1	30 hpf Tg 8.0claudinB:lynGFPzf106/ TgBACcxcr4b:F tractin mCherry zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube Library was performed according to the manufacturer's instructions single cell three prime v3 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP432326		loader:fastq load.py	CEL200317AN_zebrafish_pLLP_S3_L002_I1_001.fastq.gz CEL200317AN_zebrafish_pLLP_S3_L002_R1_001.fastq.gz CEL200317AN_zebrafish_pLLP_S3_L002_R2_001.fastq.gz	fastq fastq fastq	3881456931.0	30562653.0	GSM7165622 r6	0:8 1:28 2:91	A:853798807;C:569305743;G:651609677;T:706472540;N:14656	8	28	91		853798807	569305743	651609677	706472540	14656	SRX19948131	SRS17296333	SRA1622376	Oregon Health and Science Univ	Oregon Health and Science Univ	1	0.86918		0.17885		0.7671		0.52606		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2023-04-12	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures