run_metadata: 76793

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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
76793	SRR25374439	SRX21113459	SRS18382053	SRP450614	PRJNA996961	Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.	GSE237867	Transcriptome Analysis	Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. Single cell RNA Sequencing For single cell RNA Seq ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5.		pubmed:38924394		ExVi2Red 01 H12	GSM7655661		source name:pancreas\|tissue:pancreas\|age:4 mpf\|cell type:beta cell\|genotype:Tgins:CaMPARI\|treatment:photoconversion\|geo loc name:missing\|collection date:missing	ExVi2Red 01 H12	Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv	pancreas	The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure.	The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara	4 mpf Tgins:CaMPARI zebrafish	tissue:pancreas\|age:4 mpf\|cell type:beta cell\|genotype:Tgins:CaMPARI\|treatment:photoconversion	GSM7655661	GSM7655661: ExVi2Red 01 H12; Danio rerio; RNA Seq	GSM7655661 r1	GSM7655661	1	The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP450614		loader:fastq load.py	L21309_Track-51625_R1.fastq.gz	fastq	42457552.0	558652.0	GSM7655661 r1	0:76	A:11537651;C:9525737;G:9537176;T:11855919;N:1069	76				11537651	9525737	9537176	11855919	1069	SRX21113459	SRS18382053	SRA1676813	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.84093		0.07999		0.94458		0.51356		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq		Belgium	2023-07-20	Adult	Adult	Pancreas	Endocrine System