metadata: run_metadata: 2,521 rows where experiment.library_strategy = "RNA-Seq", tissue_curation = "Pancreas" and tissue_curation

2,521 rows where experiment.library_strategy = "RNA-Seq", tissue_curation = "Pancreas" and tissue_curation_coarse = "Endocrine System"

descending

Link	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.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
321	321	ERR977589	ERX1054572	ERS805778	ERP011346	PRJEB10140	RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish	ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55	Other	We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells.	ENA FIRST PUBLIC:2017 01 31\|ENA LAST UPDATE:2017 01 31		Beta cells from adults purified by FACS	Delta cells R3	SAMEA3498629	GIGA-R, University of Liege	ENA first public:2017 01 31\|ENA last update:2015 08 05\|External Id:SAMEA3498629\|INSDC center alias:GIGA R University of Liege\|INSDC center name:GIGA R University of Liege\|INSDC first public:2017 01 31T17:01:11Z\|INSDC last update:2015 08 05T16:56:59Z\|INSDC status:public\|Submitter Id:34\|cell type:Pancreatic Delta cells\|collected by:Estefania Tarifeño Saldivia\|common name:zebrafish\|dev stage:Adult\|isolate:Tgsst2:GFP\|lab host:ZDDM\|sample name:34							Illumina HiSeq 2000 paired end sequencing	ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:489 14	Delta R3	1	Truseq DNA Sample prep	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	ERP011346	Illumina HiSeq 2000 paired end sequencing	ENA FIRST PUBLIC:2017 01 31\|ENA LAST UPDATE:2018 11 16	NGS14-B176_SSTcells-03122013_CAGATC_L001_R1_001.fastq.gz NGS14-B176_SSTcells-03122013_CAGATC_L001_R2_001.fastq.gz	fastq fastq	17691597128.0	87582164.0	ena RUN GIGA R University of Liege 05 08 2015 16:56:42:489 14	0:101 1:101	A:4843643109;C:3683816237;G:3736882877;T:5332210638;N:95044267	101	101	4843643109	3683816237	3736882877	5332210638	95044267	ERX1054572	ERS805778	ERA463595	GIGA-R, University of Liege\|European Nucleotide Archive	GIGA-R, University of Liege	2	0.92685	0.84146	0.10249	0.11723	0.76532	0.78309	0.39721	0.43714	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2015-08-05	Adult	Adult	Pancreas	Endocrine System
330	330	ERR977580	ERX1054563	ERS805769	ERP011346	PRJEB10140	RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish	ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55	Other	We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells.	ENA FIRST PUBLIC:2017 01 31\|ENA LAST UPDATE:2017 01 31		Beta cells from adults purified by FACS	Beta cells R3	SAMEA3498620	GIGA-R, University of Liege	ENA first public:2017 01 31\|ENA last update:2015 08 05\|External Id:SAMEA3498620\|INSDC center alias:GIGA R University of Liege\|INSDC center name:GIGA R University of Liege\|INSDC first public:2017 01 31T17:01:11Z\|INSDC last update:2015 08 05T16:56:59Z\|INSDC status:public\|Submitter Id:25\|cell type:Pancreatic Beta cells\|collected by:Estefania Tarifeño Saldivia\|common name:zebrafish\|dev stage:Adult\|isolate:Tgins:GFP\|lab host:ZDDM\|sample name:25							Illumina HiSeq 2000 paired end sequencing	ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:487 5	Beta R3	1	Truseq DNA Sample prep	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	ERP011346	Illumina HiSeq 2000 paired end sequencing	ENA FIRST PUBLIC:2017 01 31\|ENA LAST UPDATE:2018 11 16	NGS14-B174_Betacells-03122013_GCCAAT_L002_R1_001.fastq.gz NGS14-B174_Betacells-03122013_GCCAAT_L002_R2_001.fastq.gz	fastq fastq	17625660086.0	87255743.0	ena RUN GIGA R University of Liege 05 08 2015 16:56:42:487 5	0:101 1:101	A:4840276660;C:3724973884;G:3755195525;T:5214977933;N:90236084	101	101	4840276660	3724973884	3755195525	5214977933	90236084	ERX1054563	ERS805769	ERA463595	GIGA-R, University of Liege\|European Nucleotide Archive	GIGA-R, University of Liege	2	0.90631	0.8718	0.11791	0.11942	0.76203	0.77638	0.53654	0.49457	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2015-08-05	Adult	Adult	Pancreas	Endocrine System
331	331	ERR977579	ERX1054562	ERS805768	ERP011346	PRJEB10140	RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish	ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55	Other	We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells.	ENA FIRST PUBLIC:2017 01 31\|ENA LAST UPDATE:2017 01 31		Beta cells from adults purified by FACS	Beta cells R2 2	SAMEA3498619	GIGA-R, University of Liege	ENA first public:2017 01 31\|ENA last update:2015 08 05\|External Id:SAMEA3498619\|INSDC center alias:GIGA R University of Liege\|INSDC center name:GIGA R University of Liege\|INSDC first public:2017 01 31T17:01:11Z\|INSDC last update:2015 08 05T16:56:59Z\|INSDC status:public\|Submitter Id:24\|cell type:Pancreatic Beta cells\|collected by:Estefania Tarifeño Saldivia\|common name:zebrafish\|dev stage:Adult\|isolate:Tgins:GFP\|lab host:ZDDM\|sample name:24							Illumina HiSeq 2000 paired end sequencing	ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:487 4	Beta R2 2	1	Truseq DNA Sample prep	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	ERP011346	Illumina HiSeq 2000 paired end sequencing	ENA FIRST PUBLIC:2017 01 31\|ENA LAST UPDATE:2018 11 16	BetaCell2_A026_ATGTCA_L004_R1_001.fastq.gz BetaCell2_A026_ATGTCA_L004_R2_001.fastq.gz	fastq fastq	8532015198.0	42237699.0	ena RUN GIGA R University of Liege 05 08 2015 16:56:42:487 4	0:101 1:101	A:2314776471;C:1823939144;G:1839244845;T:2552984556;N:1070182	101	101	2314776471	1823939144	1839244845	2552984556	1070182	ERX1054562	ERS805768	ERA463595	GIGA-R, University of Liege\|European Nucleotide Archive	GIGA-R, University of Liege	2	0.69844	0.57999	0.09124	0.07501	0.80876	0.82964	0.56023	0.5159	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2015-08-05	Adult	Adult	Pancreas	Endocrine System
332	332	ERR977578	ERX1054561	ERS805767	ERP011346	PRJEB10140	RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish	ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55	Other	We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells.	ENA FIRST PUBLIC:2017 01 31\|ENA LAST UPDATE:2017 01 31		Beta cells from adults purified by FACS	Beta cells R2 1	SAMEA3498618	GIGA-R, University of Liege	ENA first public:2017 01 31\|ENA last update:2015 08 05\|External Id:SAMEA3498618\|INSDC center alias:GIGA R University of Liege\|INSDC center name:GIGA R University of Liege\|INSDC first public:2017 01 31T17:01:11Z\|INSDC last update:2015 08 05T16:56:59Z\|INSDC status:public\|Submitter Id:23\|cell type:Pancreatic Beta cells\|collected by:Estefania Tarifeño Saldivia\|common name:zebrafish\|dev stage:Adult\|isolate:Tgins:GFP\|lab host:ZDDM\|sample name:23							Illumina HiSeq 2000 paired end sequencing	ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:487 3	Beta R2 1	1	Truseq DNA Sample prep	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	ERP011346	Illumina HiSeq 2000 paired end sequencing	ENA FIRST PUBLIC:2017 01 31\|ENA LAST UPDATE:2018 11 16	BetaCell_ATGTCA_L005_R1_001.fastq.gz BetaCell_ATGTCA_L005_R2_001.fastq.gz	fastq fastq	3250611068.0	16092134.0	ena RUN GIGA R University of Liege 05 08 2015 16:56:42:487 3	0:101 1:101	A:854826460;C:691024995;G:695294721;T:954934438;N:54530454	101	101	854826460	691024995	695294721	954934438	54530454	ERX1054561	ERS805767	ERA463595	GIGA-R, University of Liege\|European Nucleotide Archive	GIGA-R, University of Liege	2	0.67496	0.53873	0.08771	0.06606	0.80969	0.83433	0.56231	0.51717	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2015-08-05	Adult	Adult	Pancreas	Endocrine System
333	333	ERR977577	ERX1054560	ERS805766	ERP011346	PRJEB10140	RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish	ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55	Other	We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells.	ENA FIRST PUBLIC:2017 01 31\|ENA LAST UPDATE:2017 01 31		Beta cells from adults purified by FACS	Beta cells R1 2	SAMEA3498617	GIGA-R, University of Liege	ENA first public:2017 01 31\|ENA last update:2015 08 05\|External Id:SAMEA3498617\|INSDC center alias:GIGA R University of Liege\|INSDC center name:GIGA R University of Liege\|INSDC first public:2017 01 31T17:01:11Z\|INSDC last update:2015 08 05T16:56:59Z\|INSDC status:public\|Submitter Id:22\|cell type:Pancreatic Beta cells\|collected by:Estefania Tarifeño Saldivia\|common name:zebrafish\|dev stage:Adult\|isolate:Tgins:GFP\|lab host:ZDDM\|sample name:22							Illumina HiSeq 2000 paired end sequencing	ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:487 2	Beta R1 2	1	Truseq DNA Sample prep	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	ERP011346	Illumina HiSeq 2000 paired end sequencing	ENA FIRST PUBLIC:2017 01 31\|ENA LAST UPDATE:2018 11 16	BetaCell1_A003_GTCCGC_L004_R1_001.fastq.gz BetaCell1_A003_GTCCGC_L004_R2_001.fastq.gz	fastq fastq	3765102038.0	18639119.0	ena RUN GIGA R University of Liege 05 08 2015 16:56:42:487 2	0:101 1:101	A:1050226787;C:789381360;G:801049952;T:1123973291;N:470648	101	101	1050226787	789381360	801049952	1123973291	470648	ERX1054560	ERS805766	ERA463595	GIGA-R, University of Liege\|European Nucleotide Archive	GIGA-R, University of Liege	2	0.90456	0.86125	0.12934	0.13194	0.77721	0.79109	0.56708	0.53213	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2015-08-05	Adult	Adult	Pancreas	Endocrine System
334	334	ERR977576	ERX1054559	ERS805765	ERP011346	PRJEB10140	RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish	ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55	Other	We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells.	ENA FIRST PUBLIC:2017 01 31\|ENA LAST UPDATE:2017 01 31		Beta cells from adults purified by FACS	Beta cells R1 1	SAMEA3498616	GIGA-R, University of Liege	ENA first public:2017 01 31\|ENA last update:2015 08 05\|External Id:SAMEA3498616\|INSDC center alias:GIGA R University of Liege\|INSDC center name:GIGA R University of Liege\|INSDC first public:2017 01 31T17:01:11Z\|INSDC last update:2015 08 05T16:56:59Z\|INSDC status:public\|Submitter Id:21\|cell type:Pancreatic Beta cells\|collected by:Estefania Tarifeño Saldivia\|common name:zebrafish\|dev stage:Adult\|isolate:Tgins:GFP\|lab host:ZDDM\|sample name:21							Illumina HiSeq 2000 paired end sequencing	ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:486 1	Beta R1 1	1	Truseq DNA Sample prep	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	ERP011346	Illumina HiSeq 2000 paired end sequencing	ENA FIRST PUBLIC:2017 01 31\|ENA LAST UPDATE:2018 11 16	BetaCells_30000_GTCCGC_L008_R1_001.fastq.gz BetaCells_30000_GTCCGC_L008_R2_001.fastq.gz	fastq fastq	10597717092.0	52463946.0	ena RUN GIGA R University of Liege 05 08 2015 16:56:42:486 1	0:101 1:101	A:2951812422;C:2213949786;G:2252957090;T:3178649938;N:347856	101	101	2951812422	2213949786	2252957090	3178649938	347856	ERX1054559	ERS805765	ERA463595	GIGA-R, University of Liege\|European Nucleotide Archive	GIGA-R, University of Liege	2	0.90302	0.84857	0.12843	0.12749	0.77745	0.79157	0.56129	0.52011	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2015-08-05	Adult	Adult	Pancreas	Endocrine System
10002	10002	ERR6806875	ERX6430468	ERS5060069	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22		Adult zebrafish whole pancreas RNA seq replicate2 raw reads	Zebrafish Whole Pancreas RNA seq replicate2	SAMEA7301510	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301510\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Whole Pancreas RNA seq replicate2\|common name:zebrafish\|sample name:Zebrafish Whole Pancreas RNA seq replicate2\|tissue type:whole pancreas							Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:330 6	Exocrine2	1	Total RNA extracted with TRIZOL from zebrafish whole pancreas and preprared for sequencing with the TruSeq kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Exocrine_Old_1.fastq.gz	fastq	1715678250.0	34313565.0	ena RUN I3S 23 09 2021 16:43:09:330 6	0:50 1:0	A:423211245;C:429948631;G:413857387;T:448546996;N:113991	50	0	423211245	429948631	413857387	448546996	113991	ERX6430468	ERS5060069	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.94581		0.03181		0.80026		0.48102		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Pancreas	Endocrine System
10003	10003	ERR6806874	ERX6430467	ERS5060068	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22		Adult zebrafish whole pancreas RNA seq replicate1 raw reads	Zebrafish Whole Pancreas RNA seq replicate1	SAMEA7301509	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301509\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Whole Pancreas RNA seq replicate1\|common name:zebrafish\|sample name:Zebrafish Whole Pancreas RNA seq replicate1\|tissue type:whole pancreas							Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:330 5	Exocrine1	1	Total RNA extracted with TRIZOL from zebrafish whole pancreas and preprared for sequencing with the TruSeq kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Exocrine_Young_1.fastq.gz	fastq	1751070500.0	35021410.0	ena RUN I3S 23 09 2021 16:43:09:330 5	0:50 1:0	A:412303526;C:454121976;G:438481251;T:446048184;N:115563	50	0	412303526	454121976	438481251	446048184	115563	ERX6430467	ERS5060068	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.93968		0.02618		0.8003		0.58539		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Pancreas	Endocrine System
10004	10004	ERR6806873	ERX6430466	ERS5060036	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22		Adult zebrafish endocrine pancreas RNA seq replicate4 raw reads	Zebrafish Endocrine Pancreas RNA seq replicate4	SAMEA7301477	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301477\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Endocrine Pancreas RNA seq replicate4\|common name:zebrafish\|sample name:Zebrafish Endocrine Pancreas RNA seq replicate4\|tissue type:endocrine pancreas principal islet							Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:330 4	Endocrine4	1	Total RNA extracted with TRIZOL from zebrafish primary pancreatic islet and preprared for sequencing with the TruSeq kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Endocrine_Old_2.fastq.gz	fastq	1710560600.0	34211212.0	ena RUN I3S 23 09 2021 16:43:09:330 4	0:50 1:0	A:441527784;C:412091003;G:396100295;T:460728135;N:113383	50	0	441527784	412091003	396100295	460728135	113383	ERX6430466	ERS5060036	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.95616		0.04334		0.84585		0.17182		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Pancreas	Endocrine System
10005	10005	ERR6806872	ERX6430465	ERS5060035	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22		Adult zebrafish endocrine pancreas RNA seq replicate3 raw reads	Zebrafish Endocrine Pancreas RNA seq replicate3	SAMEA7301476	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301476\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Endocrine Pancreas RNA seq replicate3\|common name:zebrafish\|sample name:Zebrafish Endocrine Pancreas RNA seq replicate3\|tissue type:endocrine pancreas principal islet							Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:330 3	Endocrine3	1	Total RNA extracted with TRIZOL from zebrafish primary pancreatic islet and preprared for sequencing with the TruSeq kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Endocrine_Old_1.fastq.gz	fastq	1979582750.0	39591655.0	ena RUN I3S 23 09 2021 16:43:09:330 3	0:50 1:0	A:483713055;C:499972514;G:479484600;T:516281513;N:131068	50	0	483713055	499972514	479484600	516281513	131068	ERX6430465	ERS5060035	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.93722		0.04096		0.7559		0.52069		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Pancreas	Endocrine System
10006	10006	ERR6806871	ERX6430464	ERS5060034	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22		Adult zebrafish endocrine pancreas principal islet RNA seq raw reads replicate2	Zebrafish Endocrine Pancreas RNA seq replicate2	SAMEA7301475	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301475\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Endocrine Pancreas RNA seq replicate2\|common name:zebrafish\|sample name:Zebrafish Endocrine Pancreas RNA seq replicate2\|tissue type:endocrine pancreas principal islet							Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:329 2	Endocrine2	1	Total RNA extracted with TRIZOL from zebrafish primary pancreatic islet and preprared for sequencing with the TruSeq kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Endocrine_Young_2.fastq.gz	fastq	1846315600.0	36926312.0	ena RUN I3S 23 09 2021 16:43:09:329 2	0:50 1:0	A:466245839;C:453675875;G:433502059;T:492768958;N:122869	50	0	466245839	453675875	433502059	492768958	122869	ERX6430464	ERS5060034	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.93566		0.06945		0.74065		0.47497		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Pancreas	Endocrine System
10007	10007	ERR6806870	ERX6430463	ERS5060033	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22		Adult zebrafish endocrine pancreas principal islet RNA seq raw reads replicate1	Zebrafish Endocrine Pancreas RNA seq replicate1	SAMEA7301474	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301474\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Endocrine Pancreas RNA seq replicate1\|common name:zebrafish\|sample name:Zebrafish Endocrine Pancreas RNA seq replicate1\|tissue type:endocrine pancreas principal islet							Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:329 1	Endocrine1	1	Total RNA extracted with TRIZOL from zebrafish primary pancreatic islet and preprared for sequencing with the TruSeq kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Endocrine_Young_1.fastq.gz	fastq	1331184450.0	26623689.0	ena RUN I3S 23 09 2021 16:43:09:329 1	0:50 1:0	A:336761837;C:326693218;G:311881921;T:355763246;N:84228	50	0	336761837	326693218	311881921	355763246	84228	ERX6430463	ERS5060033	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.93154		0.07422		0.73064		0.53917		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Pancreas	Endocrine System
30776	30776	SRR28359146	SRX23964396	SRS20764037	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 E22	GSM8150156		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 E22	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150156	GSM8150156: CSN48 1 03 E22; Danio rerio; RNA Seq	GSM8150156 r1	GSM8150156	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53728_Track-95571_R1.fastq.gz L53728_Track-95571_R2.fastq.gz	fastq fastq	104878542.0	1028221.0	GSM8150156 r1	0:51 1:51	A:28863138;C:21525262;G:22453118;T:32031599;N:5425	51	51	28863138	21525262	22453118	32031599	5425	SRX23964396	SRS20764037	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.77262	0.78585	0.0988	0.10576	0.98981	0.98969	0.68036	0.67233	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30777	30777	SRR28359147	SRX23964395	SRS20764036	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 E21	GSM8150155		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 E21	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150155	GSM8150155: CSN48 1 03 E21; Danio rerio; RNA Seq	GSM8150155 r1	GSM8150155	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53727_Track-95291_R1.fastq.gz L53727_Track-95291_R2.fastq.gz	fastq fastq	121185282.0	1188091.0	GSM8150155 r1	0:51 1:51	A:33696023;C:24967708;G:26140769;T:36374401;N:6381	51	51	33696023	24967708	26140769	36374401	6381	SRX23964395	SRS20764036	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.81964	0.8273	0.07915	0.08503	0.98072	0.98082	0.5136	0.50712	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30778	30778	SRR28359148	SRX23964394	SRS20764035	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 E20	GSM8150154		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 E20	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150154	GSM8150154: CSN48 1 03 E20; Danio rerio; RNA Seq	GSM8150154 r1	GSM8150154	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53726_Track-95418_R1.fastq.gz L53726_Track-95418_R2.fastq.gz	fastq fastq	72575040.0	711520.0	GSM8150154 r1	0:51 1:51	A:20943429;C:14224819;G:14955120;T:22447601;N:4071	51	51	20943429	14224819	14955120	22447601	4071	SRX23964394	SRS20764035	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.82387	0.83093	0.08054	0.08675	0.98687	0.98721	0.5993	0.61815	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30779	30779	SRR28359149	SRX23964393	SRS20764034	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 E19	GSM8150153		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 E19	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150153	GSM8150153: CSN48 1 03 E19; Danio rerio; RNA Seq	GSM8150153 r1	GSM8150153	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53725_Track-95634_R1.fastq.gz L53725_Track-95634_R2.fastq.gz	fastq fastq	80873046.0	792873.0	GSM8150153 r1	0:51 1:51	A:23739380;C:13085794;G:15017775;T:29025944;N:4153	51	51	23739380	13085794	15017775	29025944	4153	SRX23964393	SRS20764034	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.05147	0.14716	0.0371	0.1306	0.98806	0.98833	0.56028	0.59733	51	51	B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30780	30780	SRR28359150	SRX23964392	SRS20764033	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 E18	GSM8150152		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 E18	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150152	GSM8150152: CSN48 1 03 E18; Danio rerio; RNA Seq	GSM8150152 r1	GSM8150152	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53724_Track-95288_R2.fastq.gz L53724_Track-95288_R1.fastq.gz	fastq fastq	70936512.0	695456.0	GSM8150152 r1	0:51 1:51	A:19357090;C:14845900;G:15470063;T:21259791;N:3668	51	51	19357090	14845900	15470063	21259791	3668	SRX23964392	SRS20764033	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.7423	0.75148	0.09603	0.10377	0.99066	0.99062	0.56913	0.56951	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30781	30781	SRR28359151	SRX23964391	SRS20764032	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 E17	GSM8150151		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 E17	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150151	GSM8150151: CSN48 1 03 E17; Danio rerio; RNA Seq	GSM8150151 r1	GSM8150151	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53723_Track-95437_R1.fastq.gz L53723_Track-95437_R2.fastq.gz	fastq fastq	55774620.0	546810.0	GSM8150151 r1	0:51 1:51	A:15911187;C:11099571;G:11653395;T:17107731;N:2736	51	51	15911187	11099571	11653395	17107731	2736	SRX23964391	SRS20764032	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.78444	0.80042	0.1432	0.15501	0.98204	0.98218	0.51608	0.51677	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30782	30782	SRR28359152	SRX23964390	SRS20764030	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 E16	GSM8150150		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 E16	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150150	GSM8150150: CSN48 1 03 E16; Danio rerio; RNA Seq	GSM8150150 r1	GSM8150150	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53722_Track-95347_R1.fastq.gz L53722_Track-95347_R2.fastq.gz	fastq fastq	76449000.0	749500.0	GSM8150150 r1	0:51 1:51	A:22809962;C:14680254;G:15102439;T:23852396;N:3949	51	51	22809962	14680254	15102439	23852396	3949	SRX23964390	SRS20764030	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.86893	0.87396	0.03149	0.03559	0.99212	0.99198	0.98514	0.97868	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30783	30783	SRR28359153	SRX23964389	SRS20764029	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 E15	GSM8150149		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 E15	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150149	GSM8150149: CSN48 1 03 E15; Danio rerio; RNA Seq	GSM8150149 r1	GSM8150149	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53721_Track-95493_R1.fastq.gz L53721_Track-95493_R2.fastq.gz	fastq fastq	99461424.0	975112.0	GSM8150149 r1	0:51 1:51	A:27045437;C:21070936;G:21587770;T:29752188;N:5093	51	51	27045437	21070936	21587770	29752188	5093	SRX23964389	SRS20764029	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.76782	0.77265	0.08688	0.09118	0.98681	0.98664	0.63246	0.63378	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30784	30784	SRR28359154	SRX23964388	SRS20764031	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 D14	GSM8150124		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 D14	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150124	GSM8150124: CSN48 1 03 D14; Danio rerio; RNA Seq	GSM8150124 r1	GSM8150124	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53696_Track-95353_R1.fastq.gz L53696_Track-95353_R2.fastq.gz	fastq fastq	69766878.0	683989.0	GSM8150124 r1	0:51 1:51	A:20239008;C:13266241;G:14104575;T:22153275;N:3779	51	51	20239008	13266241	14104575	22153275	3779	SRX23964388	SRS20764031	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.78176	0.78796	0.18103	0.1874	0.98186	0.9821	0.67624	0.66145	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30785	30785	SRR28359155	SRX23964387	SRS20764027	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 D13	GSM8150123		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 D13	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150123	GSM8150123: CSN48 1 03 D13; Danio rerio; RNA Seq	GSM8150123 r1	GSM8150123	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53695_Track-95522_R1.fastq.gz L53695_Track-95522_R2.fastq.gz	fastq fastq	91446672.0	896536.0	GSM8150123 r1	0:51 1:51	A:26181544;C:17663296;G:18796711;T:28800124;N:4997	51	51	26181544	17663296	18796711	28800124	4997	SRX23964387	SRS20764027	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.78134	0.7878	0.12516	0.13008	0.98644	0.9865	0.71837	0.72978	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30786	30786	SRR28359156	SRX23964386	SRS20764028	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 D12	GSM8150122		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 D12	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150122	GSM8150122: CSN48 1 03 D12; Danio rerio; RNA Seq	GSM8150122 r1	GSM8150122	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53694_Track-95365_R1.fastq.gz L53694_Track-95365_R2.fastq.gz	fastq fastq	69981894.0	686097.0	GSM8150122 r1	0:51 1:51	A:19839934;C:13755443;G:14688765;T:21694242;N:3510	51	51	19839934	13755443	14688765	21694242	3510	SRX23964386	SRS20764028	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.78924	0.79909	0.08205	0.08909	0.9847	0.98445	0.58412	0.58962	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30787	30787	SRR28359157	SRX23964385	SRS20764026	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 D11	GSM8150121		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 D11	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150121	GSM8150121: CSN48 1 03 D11; Danio rerio; RNA Seq	GSM8150121 r1	GSM8150121	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53693_Track-95450_R1.fastq.gz L53693_Track-95450_R2.fastq.gz	fastq fastq	69573792.0	682096.0	GSM8150121 r1	0:51 1:51	A:19025628;C:14356513;G:14950413;T:21237487;N:3751	51	51	19025628	14356513	14950413	21237487	3751	SRX23964385	SRS20764026	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.75688	0.77057	0.12799	0.13935	0.98652	0.98636	0.64152	0.63755	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30788	30788	SRR28359158	SRX23964384	SRS20764025	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 D10	GSM8150120		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 D10	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150120	GSM8150120: CSN48 1 03 D10; Danio rerio; RNA Seq	GSM8150120 r1	GSM8150120	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53692_Track-95404_R1.fastq.gz L53692_Track-95404_R2.fastq.gz	fastq fastq	71057382.0	696641.0	GSM8150120 r1	0:51 1:51	A:19447181;C:14614798;G:15443597;T:21548130;N:3676	51	51	19447181	14614798	15443597	21548130	3676	SRX23964384	SRS20764025	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.75621	0.77479	0.0847	0.09971	0.9881	0.98841	0.64117	0.6427	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30789	30789	SRR28359159	SRX23964383	SRS20764024	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 D09	GSM8150119		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 D09	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150119	GSM8150119: CSN48 1 03 D09; Danio rerio; RNA Seq	GSM8150119 r1	GSM8150119	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53691_Track-95318_R1.fastq.gz L53691_Track-95318_R2.fastq.gz	fastq fastq	89856084.0	880942.0	GSM8150119 r1	0:51 1:51	A:24229021;C:19039299;G:19705052;T:26877901;N:4811	51	51	24229021	19039299	19705052	26877901	4811	SRX23964383	SRS20764024	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.73565	0.74513	0.08918	0.09582	0.98882	0.98875	0.63639	0.63689	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30790	30790	SRR28359160	SRX23964382	SRS20764023	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 D08	GSM8150118		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 D08	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150118	GSM8150118: CSN48 1 03 D08; Danio rerio; RNA Seq	GSM8150118 r1	GSM8150118	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53690_Track-95414_R1.fastq.gz L53690_Track-95414_R2.fastq.gz	fastq fastq	51053856.0	500528.0	GSM8150118 r1	0:51 1:51	A:14497740;C:9903942;G:10595509;T:16053978;N:2687	51	51	14497740	9903942	10595509	16053978	2687	SRX23964382	SRS20764023	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.76986	0.77936	0.11864	0.12512	0.97264	0.97268	0.5459	0.55357	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30791	30791	SRR28359161	SRX23964381	SRS20764022	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 D07	GSM8150117		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 D07	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150117	GSM8150117: CSN48 1 03 D07; Danio rerio; RNA Seq	GSM8150117 r1	GSM8150117	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53689_Track-95464_R1.fastq.gz L53689_Track-95464_R2.fastq.gz	fastq fastq	97634706.0	957203.0	GSM8150117 r1	0:51 1:51	A:27221899;C:20175184;G:21078138;T:29154379;N:5106	51	51	27221899	20175184	21078138	29154379	5106	SRX23964381	SRS20764022	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.81639	0.82226	0.09416	0.09868	0.98492	0.98506	0.71814	0.67945	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30792	30792	SRR28359162	SRX23964380	SRS20764021	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 C22	GSM8150108		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 C22	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150108	GSM8150108: CSN48 1 03 C22; Danio rerio; RNA Seq	GSM8150108 r1	GSM8150108	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53680_Track-95514_R1.fastq.gz L53680_Track-95514_R2.fastq.gz	fastq fastq	85898790.0	842145.0	GSM8150108 r1	0:51 1:51	A:25113234;C:15409408;G:16800656;T:28570810;N:4682	51	51	25113234	15409408	16800656	28570810	4682	SRX23964380	SRS20764021	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.73097	0.73915	0.16293	0.16856	0.97788	0.97757	0.69417	0.68758	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30793	30793	SRR28359163	SRX23964379	SRS20764020	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 C21	GSM8150107		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 C21	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150107	GSM8150107: CSN48 1 03 C21; Danio rerio; RNA Seq	GSM8150107 r1	GSM8150107	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53679_Track-95616_R1.fastq.gz L53679_Track-95616_R2.fastq.gz	fastq fastq	171200064.0	1678432.0	GSM8150107 r1	0:51 1:51	A:48056238;C:34021609;G:36283975;T:52829024;N:9218	51	51	48056238	34021609	36283975	52829024	9218	SRX23964379	SRS20764020	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.74103	0.76548	0.09277	0.10863	0.98545	0.9853	0.58617	0.58598	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30794	30794	SRR28359164	SRX23964378	SRS20764019	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 C20	GSM8150106		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 C20	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150106	GSM8150106: CSN48 1 03 C20; Danio rerio; RNA Seq	GSM8150106 r1	GSM8150106	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53678_Track-95480_R1.fastq.gz L53678_Track-95480_R2.fastq.gz	fastq fastq	67253088.0	659344.0	GSM8150106 r1	0:51 1:51	A:19337100;C:12492945;G:13534630;T:21884840;N:3573	51	51	19337100	12492945	13534630	21884840	3573	SRX23964378	SRS20764019	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.72673	0.73997	0.10543	0.11545	0.98096	0.98039	0.64224	0.61696	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30795	30795	SRR28359165	SRX23964377	SRS20764018	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 C19	GSM8150105		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 C19	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150105	GSM8150105: CSN48 1 03 C19; Danio rerio; RNA Seq	GSM8150105 r1	GSM8150105	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53677_Track-95374_R1.fastq.gz L53677_Track-95374_R2.fastq.gz	fastq fastq	73674396.0	722298.0	GSM8150105 r1	0:51 1:51	A:19978507;C:15426475;G:17689441;T:20576082;N:3891	51	51	19978507	15426475	17689441	20576082	3891	SRX23964377	SRS20764018	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.77752	0.77935	0.02812	0.0303	0.97321	0.97333	0.1899	0.18724	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30796	30796	SRR28359166	SRX23964376	SRS20764017	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 C18	GSM8150104		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 C18	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150104	GSM8150104: CSN48 1 03 C18; Danio rerio; RNA Seq	GSM8150104 r1	GSM8150104	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53676_Track-95642_R1.fastq.gz L53676_Track-95642_R2.fastq.gz	fastq fastq	215575572.0	2113486.0	GSM8150104 r1	0:51 1:51	A:62335546;C:39531343;G:42959177;T:70737929;N:11577	51	51	62335546	39531343	42959177	70737929	11577	SRX23964376	SRS20764017	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.62757	0.65364	0.15539	0.17268	0.99446	0.99439	0.50474	0.50773	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30797	30797	SRR28359167	SRX23964375	SRS20764016	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 C17	GSM8150103		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 C17	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150103	GSM8150103: CSN48 1 03 C17; Danio rerio; RNA Seq	GSM8150103 r1	GSM8150103	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53675_Track-95562_R1.fastq.gz L53675_Track-95562_R2.fastq.gz	fastq fastq	84986298.0	833199.0	GSM8150103 r1	0:51 1:51	A:23272888;C:17266049;G:18271557;T:26171384;N:4420	51	51	23272888	17266049	18271557	26171384	4420	SRX23964375	SRS20764016	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.72053	0.73608	0.07211	0.08237	0.98786	0.98827	0.59708	0.59102	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30798	30798	SRR28359168	SRX23964374	SRS20764015	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 C16	GSM8150102		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 C16	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150102	GSM8150102: CSN48 1 03 C16; Danio rerio; RNA Seq	GSM8150102 r1	GSM8150102	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53674_Track-95440_R1.fastq.gz L53674_Track-95440_R2.fastq.gz	fastq fastq	54376302.0	533101.0	GSM8150102 r1	0:51 1:51	A:15467523;C:10868690;G:11508252;T:16529091;N:2746	51	51	15467523	10868690	11508252	16529091	2746	SRX23964374	SRS20764015	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.79732	0.80686	0.11376	0.1223	0.98088	0.98133	0.50056	0.50786	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30799	30799	SRR28359169	SRX23964373	SRS20764014	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 C15	GSM8150101		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 C15	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150101	GSM8150101: CSN48 1 03 C15; Danio rerio; RNA Seq	GSM8150101 r1	GSM8150101	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53673_Track-95645_R1.fastq.gz L53673_Track-95645_R2.fastq.gz	fastq fastq	49047108.0	480854.0	GSM8150101 r1	0:51 1:51	A:14358922;C:7821096;G:9574290;T:17290303;N:2497	51	51	14358922	7821096	9574290	17290303	2497	SRX23964373	SRS20764014	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.07332	0.18211	0.06412	0.1716	0.98752	0.9878	0.60524	0.60709	51	51	B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30800	30800	SRR28359170	SRX23964372	SRS20764012	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 C06	GSM8150092		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 C06	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150092	GSM8150092: CSN48 1 03 C06; Danio rerio; RNA Seq	GSM8150092 r1	GSM8150092	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53664_Track-95589_R1.fastq.gz L53664_Track-95589_R2.fastq.gz	fastq fastq	121511172.0	1191286.0	GSM8150092 r1	0:51 1:51	A:33322240;C:24518333;G:25957434;T:37706758;N:6407	51	51	33322240	24518333	25957434	37706758	6407	SRX23964372	SRS20764012	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.71937	0.73419	0.0931	0.10476	0.99145	0.99155	0.70144	0.71082	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30801	30801	SRR28359171	SRX23964371	SRS20764011	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 C05	GSM8150091		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 C05	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150091	GSM8150091: CSN48 1 03 C05; Danio rerio; RNA Seq	GSM8150091 r1	GSM8150091	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53663_Track-95466_R1.fastq.gz L53663_Track-95466_R2.fastq.gz	fastq fastq	52394136.0	513668.0	GSM8150091 r1	0:51 1:51	A:14630212;C:10551053;G:11807354;T:15402620;N:2897	51	51	14630212	10551053	11807354	15402620	2897	SRX23964371	SRS20764011	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.76894	0.77786	0.06069	0.06658	0.98242	0.98275	0.2236	0.17186	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30802	30802	SRR28359172	SRX23964370	SRS20764013	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 C04	GSM8150090		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 C04	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150090	GSM8150090: CSN48 1 03 C04; Danio rerio; RNA Seq	GSM8150090 r1	GSM8150090	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53662_Track-95349_R1.fastq.gz L53662_Track-95349_R2.fastq.gz	fastq fastq	79670568.0	781084.0	GSM8150090 r1	0:51 1:51	A:22771076;C:15643583;G:16620665;T:24630900;N:4344	51	51	22771076	15643583	16620665	24630900	4344	SRX23964370	SRS20764013	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.80374	0.806	0.08033	0.08287	0.97222	0.97218	0.61535	0.6175	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30803	30803	SRR28359173	SRX23964369	SRS20764010	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 C03	GSM8150089		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 C03	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150089	GSM8150089: CSN48 1 03 C03; Danio rerio; RNA Seq	GSM8150089 r1	GSM8150089	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53661_Track-95298_R1.fastq.gz L53661_Track-95298_R2.fastq.gz	fastq fastq	66877320.0	655660.0	GSM8150089 r1	0:51 1:51	A:19121399;C:13054001;G:13795637;T:20902909;N:3374	51	51	19121399	13054001	13795637	20902909	3374	SRX23964369	SRS20764010	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.79253	0.80117	0.0821	0.08811	0.9777	0.97792	0.69404	0.69921	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30804	30804	SRR28359174	SRX23964368	SRS20764009	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 C02	GSM8150088		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 C02	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150088	GSM8150088: CSN48 1 03 C02; Danio rerio; RNA Seq	GSM8150088 r1	GSM8150088	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53660_Track-95527_R1.fastq.gz L53660_Track-95527_R2.fastq.gz	fastq fastq	71446716.0	700458.0	GSM8150088 r1	0:51 1:51	A:20608056;C:12796514;G:14019234;T:24019077;N:3835	51	51	20608056	12796514	14019234	24019077	3835	SRX23964368	SRS20764009	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.71157	0.7141	0.16048	0.1627	0.97792	0.97845	0.67132	0.66879	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30805	30805	SRR28359175	SRX23964367	SRS20764008	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 C01	GSM8150087		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 C01	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150087	GSM8150087: CSN48 1 03 C01; Danio rerio; RNA Seq	GSM8150087 r1	GSM8150087	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53659_Track-95461_R1.fastq.gz L53659_Track-95461_R2.fastq.gz	fastq fastq	64670142.0	634021.0	GSM8150087 r1	0:51 1:51	A:17956351;C:12818976;G:13752850;T:20138633;N:3332	51	51	17956351	12818976	13752850	20138633	3332	SRX23964367	SRS20764008	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.74832	0.7561	0.09794	0.10329	0.98403	0.98388	0.40094	0.40168	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30806	30806	SRR28359176	SRX23964366	SRS20764007	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 B24	GSM8150086		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 B24	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150086	GSM8150086: CSN48 1 03 B24; Danio rerio; RNA Seq	GSM8150086 r1	GSM8150086	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53658_Track-95603_R1.fastq.gz L53658_Track-95603_R2.fastq.gz	fastq fastq	59920920.0	587460.0	GSM8150086 r1	0:51 1:51	A:17319267;C:9434358;G:12121423;T:21042551;N:3321	51	51	17319267	9434358	12121423	21042551	3321	SRX23964366	SRS20764007	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.04427	0.19448	0.03621	0.185	0.98839	0.98794	0.61065	0.61792	51	51	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30807	30807	SRR28359177	SRX23964365	SRS20764006	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 B23	GSM8150085		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 B23	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150085	GSM8150085: CSN48 1 03 B23; Danio rerio; RNA Seq	GSM8150085 r1	GSM8150085	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53657_Track-95283_R2.fastq.gz L53657_Track-95283_R1.fastq.gz	fastq fastq	53226966.0	521833.0	GSM8150085 r1	0:51 1:51	A:14941614;C:10508290;G:11101152;T:16673114;N:2796	51	51	14941614	10508290	11101152	16673114	2796	SRX23964365	SRS20764006	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.73632	0.75417	0.12668	0.14077	0.98295	0.98313	0.57551	0.57154	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30808	30808	SRR28359178	SRX23964364	SRS20764005	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 B14	GSM8150076		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 B14	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150076	GSM8150076: CSN48 1 03 B14; Danio rerio; RNA Seq	GSM8150076 r1	GSM8150076	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53648_Track-95397_R1.fastq.gz L53648_Track-95397_R2.fastq.gz	fastq fastq	76392594.0	748947.0	GSM8150076 r1	0:51 1:51	A:21364045;C:15464328;G:16352646;T:23207328;N:4247	51	51	21364045	15464328	16352646	23207328	4247	SRX23964364	SRS20764005	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.81786	0.82381	0.08799	0.09132	0.97642	0.97666	0.62228	0.61882	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30809	30809	SRR28359179	SRX23964363	SRS20764004	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 B13	GSM8150075		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 B13	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150075	GSM8150075: CSN48 1 03 B13; Danio rerio; RNA Seq	GSM8150075 r1	GSM8150075	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53647_Track-95506_R1.fastq.gz L53647_Track-95506_R2.fastq.gz	fastq fastq	36946746.0	362223.0	GSM8150075 r1	0:51 1:51	A:10280031;C:7534451;G:7970199;T:11160067;N:1998	51	51	10280031	7534451	7970199	11160067	1998	SRX23964363	SRS20764004	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.79907	0.80822	0.09071	0.0998	0.98175	0.98208	0.68971	0.64595	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30810	30810	SRR28359180	SRX23964362	SRS20764003	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 B12	GSM8150074		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 B12	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150074	GSM8150074: CSN48 1 03 B12; Danio rerio; RNA Seq	GSM8150074 r1	GSM8150074	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53646_Track-95453_R1.fastq.gz L53646_Track-95453_R2.fastq.gz	fastq fastq	85714476.0	840338.0	GSM8150074 r1	0:51 1:51	A:23566340;C:17568852;G:18323517;T:26251427;N:4340	51	51	23566340	17568852	18323517	26251427	4340	SRX23964362	SRS20764003	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.75881	0.76801	0.12155	0.12856	0.98482	0.98472	0.61286	0.62362	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30811	30811	SRR28359181	SRX23964361	SRS20764000	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 B11	GSM8150073		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 B11	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150073	GSM8150073: CSN48 1 03 B11; Danio rerio; RNA Seq	GSM8150073 r1	GSM8150073	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53645_Track-95322_R1.fastq.gz L53645_Track-95322_R2.fastq.gz	fastq fastq	60880230.0	596865.0	GSM8150073 r1	0:51 1:51	A:16894823;C:12375429;G:12826233;T:18781441;N:2304	51	51	16894823	12375429	12826233	18781441	2304	SRX23964361	SRS20764000	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.79235	0.79169	0.14033	0.14537	0.99149	0.99115	0.64974	0.6485	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30812	30812	SRR28359182	SRX23964360	SRS20764001	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 B10	GSM8150072		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 B10	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150072	GSM8150072: CSN48 1 03 B10; Danio rerio; RNA Seq	GSM8150072 r1	GSM8150072	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53644_Track-95467_R1.fastq.gz L53644_Track-95467_R2.fastq.gz	fastq fastq	98242626.0	963163.0	GSM8150072 r1	0:51 1:51	A:28157017;C:18311799;G:19643019;T:32125552;N:5239	51	51	28157017	18311799	19643019	32125552	5239	SRX23964360	SRS20764001	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.69857	0.71216	0.26037	0.27217	0.98441	0.98439	0.59596	0.58485	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30813	30813	SRR28359183	SRX23964359	SRS20764002	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 B09	GSM8150071		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 B09	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150071	GSM8150071: CSN48 1 03 B09; Danio rerio; RNA Seq	GSM8150071 r1	GSM8150071	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53643_Track-95356_R1.fastq.gz L53643_Track-95356_R2.fastq.gz	fastq fastq	72683262.0	712581.0	GSM8150071 r1	0:51 1:51	A:19574281;C:15308619;G:16971728;T:20824824;N:3810	51	51	19574281	15308619	16971728	20824824	3810	SRX23964359	SRS20764002	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.79621	0.80188	0.03212	0.03548	0.98159	0.98125	0.37766	0.43082	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30814	30814	SRR28359184	SRX23964358	SRS20763999	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 B08	GSM8150070		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 B08	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150070	GSM8150070: CSN48 1 03 B08; Danio rerio; RNA Seq	GSM8150070 r1	GSM8150070	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53642_Track-95490_R1.fastq.gz L53642_Track-95490_R2.fastq.gz	fastq fastq	48215502.0	472701.0	GSM8150070 r1	0:51 1:51	A:13666032;C:9613857;G:10126815;T:14806354;N:2444	51	51	13666032	9613857	10126815	14806354	2444	SRX23964358	SRS20763999	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.81988	0.82624	0.07106	0.07582	0.98175	0.98108	0.57602	0.57798	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30815	30815	SRR28359185	SRX23964357	SRS20763998	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 B07	GSM8150069		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 B07	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150069	GSM8150069: CSN48 1 03 B07; Danio rerio; RNA Seq	GSM8150069 r1	GSM8150069	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53641_Track-95473_R1.fastq.gz L53641_Track-95473_R2.fastq.gz	fastq fastq	76201854.0	747077.0	GSM8150069 r1	0:51 1:51	A:21033710;C:15513104;G:16188842;T:23462426;N:3772	51	51	21033710	15513104	16188842	23462426	3772	SRX23964357	SRS20763998	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.74996	0.76625	0.11529	0.12633	0.98843	0.98857	0.67337	0.6751	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30816	30816	SRR28359186	SRX23964356	SRS20763997	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 A22	GSM8150060		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 A22	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150060	GSM8150060: CSN48 1 03 A22; Danio rerio; RNA Seq	GSM8150060 r1	GSM8150060	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53632_Track-95579_R1.fastq.gz L53632_Track-95579_R2.fastq.gz	fastq fastq	89337312.0	875856.0	GSM8150060 r1	0:51 1:51	A:24279913;C:18508911;G:19215997;T:27327967;N:4524	51	51	24279913	18508911	19215997	27327967	4524	SRX23964356	SRS20763997	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.77307	0.78079	0.08474	0.08819	0.98496	0.98555	0.60362	0.59775	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30817	30817	SRR28359187	SRX23964355	SRS20763996	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 A21	GSM8150059		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 A21	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150059	GSM8150059: CSN48 1 03 A21; Danio rerio; RNA Seq	GSM8150059 r1	GSM8150059	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53631_Track-95546_R1.fastq.gz L53631_Track-95546_R2.fastq.gz	fastq fastq	102868938.0	1008519.0	GSM8150059 r1	0:51 1:51	A:28279557;C:21161886;G:21755461;T:31666533;N:5501	51	51	28279557	21161886	21755461	31666533	5501	SRX23964355	SRS20763996	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.75403	0.76348	0.13488	0.13978	0.98675	0.98723	0.61677	0.61653	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30818	30818	SRR28359188	SRX23964354	SRS20763995	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 A20	GSM8150058		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 A20	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150058	GSM8150058: CSN48 1 03 A20; Danio rerio; RNA Seq	GSM8150058 r1	GSM8150058	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53630_Track-95543_R1.fastq.gz L53630_Track-95543_R2.fastq.gz	fastq fastq	59958762.0	587831.0	GSM8150058 r1	0:51 1:51	A:17881823;C:10575047;G:11761109;T:19737967;N:2816	51	51	17881823	10575047	11761109	19737967	2816	SRX23964354	SRS20763995	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.71592	0.74628	0.02396	0.03109	0.99245	0.99251	0.92743	0.92775	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30819	30819	SRR28359189	SRX23964353	SRS20763994	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 A19	GSM8150057		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 A19	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150057	GSM8150057: CSN48 1 03 A19; Danio rerio; RNA Seq	GSM8150057 r1	GSM8150057	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53629_Track-95580_R1.fastq.gz L53629_Track-95580_R2.fastq.gz	fastq fastq	83836350.0	821925.0	GSM8150057 r1	0:51 1:51	A:23566723;C:16925562;G:17589346;T:25750439;N:4280	51	51	23566723	16925562	17589346	25750439	4280	SRX23964353	SRS20763994	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.73931	0.75043	0.11385	0.12193	0.98557	0.98557	0.63327	0.63481	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30820	30820	SRR28359190	SRX23964352	SRS20763991	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 A18	GSM8150056		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 A18	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150056	GSM8150056: CSN48 1 03 A18; Danio rerio; RNA Seq	GSM8150056 r1	GSM8150056	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53628_Track-95573_R1.fastq.gz L53628_Track-95573_R2.fastq.gz	fastq fastq	47908686.0	469693.0	GSM8150056 r1	0:51 1:51	A:13941866;C:9036815;G:9616683;T:15310786;N:2536	51	51	13941866	9036815	9616683	15310786	2536	SRX23964352	SRS20763991	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.73338	0.75945	0.01988	0.03615	0.99064	0.99062	0.88101	0.86842	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30821	30821	SRR28359191	SRX23964351	SRS20763993	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 A17	GSM8150055		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 A17	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150055	GSM8150055: CSN48 1 03 A17; Danio rerio; RNA Seq	GSM8150055 r1	GSM8150055	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53627_Track-95648_R1.fastq.gz L53627_Track-95648_R2.fastq.gz	fastq fastq	48067296.0	471248.0	GSM8150055 r1	0:51 1:51	A:14258002;C:7716733;G:8570836;T:17519000;N:2725	51	51	14258002	7716733	8570836	17519000	2725	SRX23964351	SRS20763993	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.03558	0.10254	0.01613	0.07956	0.98346	0.98366	0.62736	0.61877	51	51	B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30822	30822	SRR28359192	SRX23964350	SRS20763990	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 A16	GSM8150054		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 A16	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150054	GSM8150054: CSN48 1 03 A16; Danio rerio; RNA Seq	GSM8150054 r1	GSM8150054	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53626_Track-95285_R1.fastq.gz L53626_Track-95285_R2.fastq.gz	fastq fastq	64520100.0	632550.0	GSM8150054 r1	0:51 1:51	A:18529980;C:12360945;G:13126104;T:20499523;N:3548	51	51	18529980	12360945	13126104	20499523	3548	SRX23964350	SRS20763990	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.79225	0.79957	0.09612	0.09923	0.98565	0.98569	0.68585	0.68805	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30823	30823	SRR28359193	SRX23964349	SRS20763992	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 A15	GSM8150053		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 A15	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150053	GSM8150053: CSN48 1 03 A15; Danio rerio; RNA Seq	GSM8150053 r1	GSM8150053	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53625_Track-95310_R1.fastq.gz L53625_Track-95310_R2.fastq.gz	fastq fastq	57464964.0	563382.0	GSM8150053 r1	0:51 1:51	A:16027163;C:9875941;G:11249945;T:20308844;N:3071	51	51	16027163	9875941	11249945	20308844	3071	SRX23964349	SRS20763992	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.54793	0.56093	0.14665	0.15373	0.97423	0.97374	0.52447	0.52236	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30824	30824	SRR28359194	SRX23964348	SRS20763987	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 A06	GSM8150044		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 A06	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150044	GSM8150044: CSN48 1 03 A06; Danio rerio; RNA Seq	GSM8150044 r1	GSM8150044	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53616_Track-95627_R1.fastq.gz L53616_Track-95627_R2.fastq.gz	fastq fastq	42204234.0	413767.0	GSM8150044 r1	0:51 1:51	A:12167972;C:7098285;G:8516860;T:14418918;N:2199	51	51	12167972	7098285	8516860	14418918	2199	SRX23964348	SRS20763987	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.01728	0.13044	0.0054	0.11743	0.98835	0.98813	0.55491	0.55686	51	51	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30825	30825	SRR28359195	SRX23964347	SRS20763988	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 A05	GSM8150043		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 A05	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150043	GSM8150043: CSN48 1 03 A05; Danio rerio; RNA Seq	GSM8150043 r1	GSM8150043	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53615_Track-95570_R1.fastq.gz L53615_Track-95570_R2.fastq.gz	fastq fastq	60711318.0	595209.0	GSM8150043 r1	0:51 1:51	A:16616267;C:12702862;G:12998651;T:18390580;N:2958	51	51	16616267	12702862	12998651	18390580	2958	SRX23964347	SRS20763988	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.74171	0.75015	0.09281	0.09756	0.98196	0.98135	0.61594	0.6145	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30826	30826	SRR28359196	SRX23964346	SRS20763989	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 A04	GSM8150042		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 A04	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150042	GSM8150042: CSN48 1 03 A04; Danio rerio; RNA Seq	GSM8150042 r1	GSM8150042	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53614_Track-95647_R1.fastq.gz L53614_Track-95647_R2.fastq.gz	fastq fastq	25999596.0	254898.0	GSM8150042 r1	0:51 1:51	A:7736401;C:4216599;G:4559315;T:9486137;N:1144	51	51	7736401	4216599	4559315	9486137	1144	SRX23964346	SRS20763989	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.02907	0.09609	0.00643	0.06909	0.98064	0.98019	0.59162	0.61734	51	51	B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30827	30827	SRR28359197	SRX23964345	SRS20763985	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 A03	GSM8150041		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 A03	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150041	GSM8150041: CSN48 1 03 A03; Danio rerio; RNA Seq	GSM8150041 r1	GSM8150041	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53613_Track-95474_R1.fastq.gz L53613_Track-95474_R2.fastq.gz	fastq fastq	74797620.0	733310.0	GSM8150041 r1	0:51 1:51	A:20648666;C:15688335;G:16673606;T:21782908;N:4105	51	51	20648666	15688335	16673606	21782908	4105	SRX23964345	SRS20763985	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.80802	0.81136	0.0624	0.06518	0.97928	0.9792	0.60689	0.60864	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30828	30828	SRR28359198	SRX23964344	SRS20763986	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 A02	GSM8150040		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 A02	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150040	GSM8150040: CSN48 1 03 A02; Danio rerio; RNA Seq	GSM8150040 r1	GSM8150040	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53612_Track-95321_R1.fastq.gz L53612_Track-95321_R2.fastq.gz	fastq fastq	67447806.0	661253.0	GSM8150040 r1	0:51 1:51	A:19270398;C:12732437;G:13850269;T:21591414;N:3288	51	51	19270398	12732437	13850269	21591414	3288	SRX23964344	SRS20763986	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.73104	0.75072	0.13206	0.14505	0.97626	0.97648	0.54313	0.47631	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30829	30829	SRR28359199	SRX23964343	SRS20763984	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 1 03 A01	GSM8150039		tissue:beta cells\|cell type:beta cells\|treatment:CSN48 1\|geo loc name:missing\|collection date:missing	CSN48 1 03 A01	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48 1	GSM8150039	GSM8150039: CSN48 1 03 A01; Danio rerio; RNA Seq	GSM8150039 r1	GSM8150039	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53611_Track-95455_R1.fastq.gz L53611_Track-95455_R2.fastq.gz	fastq fastq	77367510.0	758505.0	GSM8150039 r1	0:51 1:51	A:21309760;C:15498935;G:16220238;T:24334550;N:4027	51	51	21309760	15498935	16220238	24334550	4027	SRX23964343	SRS20763984	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.72269	0.73574	0.13644	0.14483	0.97693	0.97678	0.64678	0.65363	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30830	30830	SRR28359200	SRX23964342	SRS20763983	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		RNA 02 G11	GSM8150038		tissue:beta cells\|cell type:beta cells\|treatment: \|geo loc name:missing\|collection date:missing	RNA 02 G11	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:	GSM8150038	GSM8150038: RNA 02 G11; Danio rerio; RNA Seq	GSM8150038 r1	GSM8150038	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53609_Track-94987_R1.fastq.gz L53609_Track-94987_R2.fastq.gz	fastq fastq	61240392.0	600396.0	GSM8150038 r1	0:51 1:51	A:16426906;C:13172096;G:13880608;T:17757981;N:2801	51	51	16426906	13172096	13880608	17757981	2801	SRX23964342	SRS20763983	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.00606	0.00847	0.00186	0.00408	0.99391	0.9934	0.61997	0.6247	51	51	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30831	30831	SRR28359201	SRX23964341	SRS20763982	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 G10	GSM8150037		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 G10	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8150037	GSM8150037: CSN24 02 G10; Danio rerio; RNA Seq	GSM8150037 r1	GSM8150037	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53608_Track-95181_R1.fastq.gz L53608_Track-95181_R2.fastq.gz	fastq fastq	108348684.0	1062242.0	GSM8150037 r1	0:51 1:51	A:30298833;C:22284186;G:23138502;T:32621431;N:5732	51	51	30298833	22284186	23138502	32621431	5732	SRX23964341	SRS20763982	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.81665	0.82026	0.10911	0.111	0.9903	0.99022	0.58375	0.60752	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30832	30832	SRR28359202	SRX23964340	SRS20763981	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 F17	GSM8150020		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 F17	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8150020	GSM8150020: CSN24 02 F17; Danio rerio; RNA Seq	GSM8150020 r1	GSM8150020	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53591_Track-95206_R1.fastq.gz L53591_Track-95206_R2.fastq.gz	fastq fastq	86279862.0	845881.0	GSM8150020 r1	0:51 1:51	A:24115181;C:17714131;G:19964968;T:24482228;N:3354	51	51	24115181	17714131	19964968	24482228	3354	SRX23964340	SRS20763981	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.80701	0.81935	0.05082	0.05296	0.99001	0.98916	0.20716	0.20255	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30833	30833	SRR28359203	SRX23964339	SRS20763980	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 F16	GSM8150019		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 F16	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8150019	GSM8150019: CSN24 02 F16; Danio rerio; RNA Seq	GSM8150019 r1	GSM8150019	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53590_Track-95236_R1.fastq.gz L53590_Track-95236_R2.fastq.gz	fastq fastq	52062228.0	510414.0	GSM8150019 r1	0:51 1:51	A:14020180;C:10872213;G:11468886;T:15698256;N:2693	51	51	14020180	10872213	11468886	15698256	2693	SRX23964339	SRS20763980	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.73918	0.76144	0.08666	0.10335	0.99164	0.99172	0.62609	0.62128	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30834	30834	SRR28359204	SRX23964338	SRS20763979	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 F15	GSM8150018		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 F15	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8150018	GSM8150018: CSN24 02 F15; Danio rerio; RNA Seq	GSM8150018 r1	GSM8150018	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53589_Track-95141_R1.fastq.gz L53589_Track-95141_R2.fastq.gz	fastq fastq	77157492.0	756446.0	GSM8150018 r1	0:51 1:51	A:21605693;C:15599581;G:16432852;T:23515612;N:3754	51	51	21605693	15599581	16432852	23515612	3754	SRX23964338	SRS20763979	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.74476	0.74702	0.10865	0.11076	0.98652	0.9862	0.44979	0.44751	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30835	30835	SRR28359205	SRX23964337	SRS20763978	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 F14	GSM8150017		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 F14	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8150017	GSM8150017: CSN24 02 F14; Danio rerio; RNA Seq	GSM8150017 r1	GSM8150017	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53588_Track-95126_R1.fastq.gz L53588_Track-95126_R2.fastq.gz	fastq fastq	53797452.0	527426.0	GSM8150017 r1	0:51 1:51	A:15116683;C:10915128;G:11435804;T:16327174;N:2663	51	51	15116683	10915128	11435804	16327174	2663	SRX23964337	SRS20763978	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.79782	0.80616	0.07566	0.08202	0.98723	0.9876	0.63965	0.6399	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30836	30836	SRR28359206	SRX23964336	SRS20763977	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 F13	GSM8150016		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 F13	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8150016	GSM8150016: CSN24 02 F13; Danio rerio; RNA Seq	GSM8150016 r1	GSM8150016	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53587_Track-95258_R1.fastq.gz L53587_Track-95258_R2.fastq.gz	fastq fastq	94360302.0	925101.0	GSM8150016 r1	0:51 1:51	A:25592436;C:19902737;G:20439380;T:28420944;N:4805	51	51	25592436	19902737	20439380	28420944	4805	SRX23964336	SRS20763977	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.77378	0.78037	0.12707	0.1297	0.99206	0.99182	0.61719	0.62462	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30837	30837	SRR28359207	SRX23964335	SRS20763976	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 F12	GSM8150015		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 F12	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8150015	GSM8150015: CSN24 02 F12; Danio rerio; RNA Seq	GSM8150015 r1	GSM8150015	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53586_Track-95184_R1.fastq.gz L53586_Track-95184_R2.fastq.gz	fastq fastq	62354844.0	611322.0	GSM8150015 r1	0:51 1:51	A:16894234;C:13102917;G:13985509;T:18368881;N:3303	51	51	16894234	13102917	13985509	18368881	3303	SRX23964335	SRS20763976	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.77413	0.77856	0.0563	0.06016	0.97601	0.97546	0.52098	0.52409	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30838	30838	SRR28359208	SRX23964334	SRS20763975	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 F11	GSM8150014		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 F11	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8150014	GSM8150014: CSN24 02 F11; Danio rerio; RNA Seq	GSM8150014 r1	GSM8150014	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53585_Track-95282_R1.fastq.gz L53585_Track-95282_R2.fastq.gz	fastq fastq	134866134.0	1322217.0	GSM8150014 r1	0:51 1:51	A:36606180;C:28153427;G:29082203;T:41017328;N:6996	51	51	36606180	28153427	29082203	41017328	6996	SRX23964334	SRS20763975	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.78038	0.78847	0.103	0.10673	0.99022	0.99026	0.63847	0.64824	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30839	30839	SRR28359209	SRX23964333	SRS20763973	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 F10	GSM8150013		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 F10	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8150013	GSM8150013: CSN24 02 F10; Danio rerio; RNA Seq	GSM8150013 r1	GSM8150013	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53584_Track-94961_R1.fastq.gz L53584_Track-94961_R2.fastq.gz	fastq fastq	57289218.0	561659.0	GSM8150013 r1	0:51 1:51	A:15654996;C:12067784;G:13483977;T:16079504;N:2957	51	51	15654996	12067784	13483977	16079504	2957	SRX23964333	SRS20763973	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.78546	0.78801	0.03275	0.0365	0.98451	0.98484	0.18731	0.18714	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30840	30840	SRR28359210	SRX23964332	SRS20763974	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 F01	GSM8150004		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 F01	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8150004	GSM8150004: CSN24 02 F01; Danio rerio; RNA Seq	GSM8150004 r1	GSM8150004	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53575_Track-95159_R1.fastq.gz L53575_Track-95159_R2.fastq.gz	fastq fastq	120780648.0	1184124.0	GSM8150004 r1	0:51 1:51	A:32680701;C:24675276;G:25705829;T:37712522;N:6320	51	51	32680701	24675276	25705829	37712522	6320	SRX23964332	SRS20763974	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.74064	0.74741	0.09215	0.09447	0.98746	0.98764	0.6778	0.66742	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30841	30841	SRR28359211	SRX23964331	SRS20763972	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 E24	GSM8150003		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 E24	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8150003	GSM8150003: CSN24 02 E24; Danio rerio; RNA Seq	GSM8150003 r1	GSM8150003	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53574_Track-95235_R1.fastq.gz L53574_Track-95235_R2.fastq.gz	fastq fastq	125646150.0	1231825.0	GSM8150003 r1	0:51 1:51	A:34906622;C:25653760;G:26843705;T:38235468;N:6595	51	51	34906622	25653760	26843705	38235468	6595	SRX23964331	SRS20763972	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.79136	0.79591	0.11781	0.1209	0.99275	0.99261	0.59738	0.60471	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30842	30842	SRR28359212	SRX23964330	SRS20763971	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 E23	GSM8150002		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 E23	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8150002	GSM8150002: CSN24 02 E23; Danio rerio; RNA Seq	GSM8150002 r1	GSM8150002	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53573_Track-95222_R1.fastq.gz L53573_Track-95222_R2.fastq.gz	fastq fastq	102050286.0	1000493.0	GSM8150002 r1	0:51 1:51	A:28856641;C:20351972;G:21425480;T:31410880;N:5313	51	51	28856641	20351972	21425480	31410880	5313	SRX23964330	SRS20763971	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.77509	0.78297	0.13105	0.13959	0.98275	0.98236	0.57536	0.56425	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30843	30843	SRR28359213	SRX23964329	SRS20763970	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 E22	GSM8150001		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 E22	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8150001	GSM8150001: CSN24 02 E22; Danio rerio; RNA Seq	GSM8150001 r1	GSM8150001	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53572_Track-95208_R1.fastq.gz L53572_Track-95208_R2.fastq.gz	fastq fastq	93339384.0	915092.0	GSM8150001 r1	0:51 1:51	A:24881598;C:19769054;G:20522772;T:28161697;N:4263	51	51	24881598	19769054	20522772	28161697	4263	SRX23964329	SRS20763970	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.79486	0.79815	0.0588	0.06066	0.99391	0.99375	0.61742	0.62514	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30844	30844	SRR28359214	SRX23964328	SRS20763969	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 E21	GSM8150000		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 E21	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8150000	GSM8150000: CSN24 02 E21; Danio rerio; RNA Seq	GSM8150000 r1	GSM8150000	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53571_Track-95100_R1.fastq.gz L53571_Track-95100_R2.fastq.gz	fastq fastq	81079596.0	794898.0	GSM8150000 r1	0:51 1:51	A:22871371;C:16291248;G:17451823;T:24461074;N:4080	51	51	22871371	16291248	17451823	24461074	4080	SRX23964328	SRS20763969	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.76031	0.78541	0.13661	0.15665	0.98693	0.98683	0.524	0.53378	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30845	30845	SRR28359215	SRX23964327	SRS20763968	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 E20	GSM8149999		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 E20	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8149999	GSM8149999: CSN24 02 E20; Danio rerio; RNA Seq	GSM8149999 r1	GSM8149999	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53570_Track-95253_R1.fastq.gz L53570_Track-95253_R2.fastq.gz	fastq fastq	110380524.0	1082162.0	GSM8149999 r1	0:51 1:51	A:29965518;C:23223337;G:24025378;T:33160713;N:5578	51	51	29965518	23223337	24025378	33160713	5578	SRX23964327	SRS20763968	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.80146	0.80582	0.09058	0.09163	0.99153	0.99155	0.59927	0.60152	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30846	30846	SRR28359216	SRX23964326	SRS20763967	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 E19	GSM8149998		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 E19	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8149998	GSM8149998: CSN24 02 E19; Danio rerio; RNA Seq	GSM8149998 r1	GSM8149998	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53569_Track-95196_R1.fastq.gz L53569_Track-95196_R2.fastq.gz	fastq fastq	69006060.0	676530.0	GSM8149998 r1	0:51 1:51	A:18708547;C:14544311;G:15053174;T:20696747;N:3281	51	51	18708547	14544311	15053174	20696747	3281	SRX23964326	SRS20763967	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.79623	0.80729	0.10708	0.11406	0.98378	0.98388	0.63419	0.64935	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30847	30847	SRR28359217	SRX23964325	SRS20763965	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 E18	GSM8149997		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 E18	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8149997	GSM8149997: CSN24 02 E18; Danio rerio; RNA Seq	GSM8149997 r1	GSM8149997	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53568_Track-95096_R1.fastq.gz L53568_Track-95096_R2.fastq.gz	fastq fastq	99737232.0	977816.0	GSM8149997 r1	0:51 1:51	A:26637824;C:21626541;G:22174230;T:29293509;N:5128	51	51	26637824	21626541	22174230	29293509	5128	SRX23964325	SRS20763965	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.81323	0.82081	0.05142	0.05469	0.98796	0.98778	0.60536	0.61653	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30848	30848	SRR28359218	SRX23964324	SRS20763964	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 E09	GSM8149988		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 E09	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8149988	GSM8149988: CSN24 02 E09; Danio rerio; RNA Seq	GSM8149988 r1	GSM8149988	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53559_Track-95194_R1.fastq.gz L53559_Track-95194_R2.fastq.gz	fastq fastq	163634418.0	1604259.0	GSM8149988 r1	0:51 1:51	A:44510452;C:34830439;G:36037266;T:48247463;N:8798	51	51	44510452	34830439	36037266	48247463	8798	SRX23964324	SRS20763964	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.81161	0.81908	0.10681	0.11049	0.98541	0.98508	0.61527	0.61898	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30849	30849	SRR28359219	SRX23964323	SRS20763966	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 E08	GSM8149987		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 E08	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8149987	GSM8149987: CSN24 02 E08; Danio rerio; RNA Seq	GSM8149987 r1	GSM8149987	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53558_Track-95209_R1.fastq.gz L53558_Track-95209_R2.fastq.gz	fastq fastq	57472104.0	563452.0	GSM8149987 r1	0:51 1:51	A:15516019;C:11920636;G:12819202;T:17212927;N:3320	51	51	15516019	11920636	12819202	17212927	3320	SRX23964323	SRS20763966	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.77941	0.80237	0.11606	0.13655	0.98843	0.98802	0.63415	0.6372	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30850	30850	SRR28359220	SRX23964322	SRS20763962	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 E07	GSM8149986		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 E07	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8149986	GSM8149986: CSN24 02 E07; Danio rerio; RNA Seq	GSM8149986 r1	GSM8149986	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53557_Track-95060_R1.fastq.gz L53557_Track-95060_R2.fastq.gz	fastq fastq	84329724.0	826762.0	GSM8149986 r1	0:51 1:51	A:23213591;C:17425659;G:18317338;T:25368637;N:4499	51	51	23213591	17425659	18317338	25368637	4499	SRX23964322	SRS20763962	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.77061	0.77727	0.10045	0.10712	0.98121	0.98068	0.56772	0.60046	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30851	30851	SRR28359221	SRX23964321	SRS20763963	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 E06	GSM8149985		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 E06	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8149985	GSM8149985: CSN24 02 E06; Danio rerio; RNA Seq	GSM8149985 r1	GSM8149985	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53556_Track-95157_R1.fastq.gz L53556_Track-95157_R2.fastq.gz	fastq fastq	90084054.0	883177.0	GSM8149985 r1	0:51 1:51	A:24491087;C:18640738;G:19792986;T:27154578;N:4665	51	51	24491087	18640738	19792986	27154578	4665	SRX23964321	SRS20763963	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.78647	0.79489	0.08515	0.09456	0.98849	0.98857	0.63931	0.66604	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30852	30852	SRR28359222	SRX23964320	SRS20763961	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 E05	GSM8149984		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 E05	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8149984	GSM8149984: CSN24 02 E05; Danio rerio; RNA Seq	GSM8149984 r1	GSM8149984	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53555_Track-94966_R1.fastq.gz L53555_Track-94966_R2.fastq.gz	fastq fastq	125602392.0	1231396.0	GSM8149984 r1	0:51 1:51	A:34921102;C:25913321;G:27652602;T:37108830;N:6537	51	51	34921102	25913321	27652602	37108830	6537	SRX23964320	SRS20763961	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.80211	0.81923	0.07468	0.08725	0.98096	0.98141	0.6085	0.60656	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30853	30853	SRR28359223	SRX23964319	SRS20763960	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 E04	GSM8149983		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 E04	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8149983	GSM8149983: CSN24 02 E04; Danio rerio; RNA Seq	GSM8149983 r1	GSM8149983	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53554_Track-95175_R1.fastq.gz L53554_Track-95175_R2.fastq.gz	fastq fastq	138146148.0	1354374.0	GSM8149983 r1	0:51 1:51	A:37652275;C:28730826;G:30345873;T:41409667;N:7507	51	51	37652275	28730826	30345873	41409667	7507	SRX23964319	SRS20763960	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.78803	0.80111	0.11623	0.12673	0.98693	0.98691	0.59478	0.59626	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30854	30854	SRR28359224	SRX23964318	SRS20763959	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 E03	GSM8149982		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 E03	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8149982	GSM8149982: CSN24 02 E03; Danio rerio; RNA Seq	GSM8149982 r1	GSM8149982	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53553_Track-95229_R1.fastq.gz L53553_Track-95229_R2.fastq.gz	fastq fastq	43340718.0	424909.0	GSM8149982 r1	0:51 1:51	A:12414298;C:8301959;G:8947793;T:13674457;N:2211	51	51	12414298	8301959	8947793	13674457	2211	SRX23964318	SRS20763959	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.77187	0.78279	0.09554	0.10234	0.96988	0.96907	0.68183	0.68002	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30855	30855	SRR28359225	SRX23964317	SRS20763957	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 E02	GSM8149981		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 E02	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8149981	GSM8149981: CSN24 02 E02; Danio rerio; RNA Seq	GSM8149981 r1	GSM8149981	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53552_Track-95270_R1.fastq.gz L53552_Track-95270_R2.fastq.gz	fastq fastq	54583770.0	535135.0	GSM8149981 r1	0:51 1:51	A:15121800;C:11180657;G:11546149;T:16733328;N:1836	51	51	15121800	11180657	11546149	16733328	1836	SRX23964317	SRS20763957	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.75063	0.74772	0.08009	0.08597	0.99226	0.99174	0.60001	0.64726	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30856	30856	SRR28359226	SRX23964316	SRS20763958	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 D17	GSM8149972		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 D17	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8149972	GSM8149972: CSN24 02 D17; Danio rerio; RNA Seq	GSM8149972 r1	GSM8149972	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53543_Track-95221_R1.fastq.gz L53543_Track-95221_R2.fastq.gz	fastq fastq	96396936.0	945068.0	GSM8149972 r1	0:51 1:51	A:27035084;C:19609718;G:20326917;T:29420013;N:5204	51	51	27035084	19609718	20326917	29420013	5204	SRX23964316	SRS20763958	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.78575	0.79348	0.10773	0.11065	0.9907	0.99084	0.62675	0.61548	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30857	30857	SRR28359227	SRX23964315	SRS20763956	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 D16	GSM8149971		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 D16	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8149971	GSM8149971: CSN24 02 D16; Danio rerio; RNA Seq	GSM8149971 r1	GSM8149971	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53542_Track-95264_R1.fastq.gz L53542_Track-95264_R2.fastq.gz	fastq fastq	96110826.0	942263.0	GSM8149971 r1	0:51 1:51	A:25901191;C:20364226;G:20916556;T:28924084;N:4769	51	51	25901191	20364226	20916556	28924084	4769	SRX23964315	SRS20763956	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.79762	0.80618	0.11011	0.11552	0.99375	0.99346	0.66749	0.66702	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30858	30858	SRR28359228	SRX23964314	SRS20763955	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 D15	GSM8149970		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 D15	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8149970	GSM8149970: CSN24 02 D15; Danio rerio; RNA Seq	GSM8149970 r1	GSM8149970	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53541_Track-95201_R1.fastq.gz L53541_Track-95201_R2.fastq.gz	fastq fastq	112977342.0	1107621.0	GSM8149970 r1	0:51 1:51	A:31316984;C:23180824;G:23954892;T:34518677;N:5965	51	51	31316984	23180824	23954892	34518677	5965	SRX23964314	SRS20763955	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.80236	0.81225	0.09467	0.09898	0.98798	0.98792	0.59556	0.60165	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30859	30859	SRR28359229	SRX23964313	SRS20763954	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 D14	GSM8149969		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 D14	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8149969	GSM8149969: CSN24 02 D14; Danio rerio; RNA Seq	GSM8149969 r1	GSM8149969	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53540_Track-95238_R1.fastq.gz L53540_Track-95238_R2.fastq.gz	fastq fastq	102919530.0	1009015.0	GSM8149969 r1	0:51 1:51	A:28150047;C:21734378;G:22351140;T:30678625;N:5340	51	51	28150047	21734378	22351140	30678625	5340	SRX23964313	SRS20763954	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.80227	0.81098	0.09599	0.10126	0.98916	0.98912	0.60568	0.60515	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30860	30860	SRR28359230	SRX23964312	SRS20763952	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 D13	GSM8149968		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 D13	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8149968	GSM8149968: CSN24 02 D13; Danio rerio; RNA Seq	GSM8149968 r1	GSM8149968	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53539_Track-95168_R1.fastq.gz L53539_Track-95168_R2.fastq.gz	fastq fastq	107626320.0	1055160.0	GSM8149968 r1	0:51 1:51	A:30184242;C:21948089;G:22592041;T:32896285;N:5663	51	51	30184242	21948089	22592041	32896285	5663	SRX23964312	SRS20763952	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.80741	0.81187	0.11977	0.12059	0.98744	0.98748	0.63704	0.63196	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30861	30861	SRR28359231	SRX23964311	SRS20763953	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 D12	GSM8149967		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 D12	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8149967	GSM8149967: CSN24 02 D12; Danio rerio; RNA Seq	GSM8149967 r1	GSM8149967	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53538_Track-95179_R1.fastq.gz L53538_Track-95179_R2.fastq.gz	fastq fastq	88955730.0	872115.0	GSM8149967 r1	0:51 1:51	A:24731175;C:18348363;G:19047295;T:26824445;N:4452	51	51	24731175	18348363	19047295	26824445	4452	SRX23964311	SRS20763953	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.78236	0.78697	0.14225	0.14606	0.98928	0.98884	0.57192	0.56974	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30862	30862	SRR28359232	SRX23964310	SRS20763951	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN24 02 D11	GSM8149966		tissue:beta cells\|cell type:beta cells\|treatment:CSN24\|geo loc name:missing\|collection date:missing	CSN24 02 D11	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN24	GSM8149966	GSM8149966: CSN24 02 D11; Danio rerio; RNA Seq	GSM8149966 r1	GSM8149966	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53537_Track-95146_R1.fastq.gz L53537_Track-95146_R2.fastq.gz	fastq fastq	133286052.0	1306726.0	GSM8149966 r1	0:51 1:51	A:36989885;C:27812176;G:28601689;T:39874764;N:7538	51	51	36989885	27812176	28601689	39874764	7538	SRX23964310	SRS20763951	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.83708	0.84176	0.09809	0.10024	0.98717	0.98699	0.55011	0.62275	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System
30863	30863	SRR28359059	SRX23964309	SRS20763949	SRP495499	PRJNA1088503	Investigating the transcriptional heterogeneity of the beta cells experiencing Ca2+ excitotoxicity	GSE261729	Transcriptome Analysis	Beta cells are remarkably heterogeneous. However beta cells response to chronic stress at a single cell level remains largely unknown. Here we used a chemo genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. Vulnerable beta cells that progressed towards death showed upregulation of genes implicated in apoptosis inflammation and immune system activation. The resilient beta cells that evaded the stress showed increased expression aldh1a3 a canonical marker of mammalian beta cell dedifferentiation. Overall design: We used three different treatment groups for this study. Tgins:Kaede larvae n=20 treated with capsaicin csn for 48 hours i.e. from 3 dpf to 5 dpf dpf were used as control. Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 24 hours i.e. from 4 dpf to 5 dpf were used to identify genes involved in immediate stress response and Tgins:TRPV;Tgins:Kaede larvae n=20 treated with csn for 48 hours i.e. from 3 dpf to 5 dpf were used to identify the genes involved in chronic stress response. Post csn treatment pancreatic islets from the larvae were manually dissected and then subsequently dissociated via enzymatic digestion. Post dissociation the beta cells were stained with calcein viability marker dye and FACS sorted. Individual beta cells were collected in a 384 well plate and their transcriptomes were profiled using smart seq2. RNA 01 H19 RNA 02 G11 RNA 03 P18 do not correspond to the other samples eg Ctrl CNS24 CNS48 2.		pubmed:39762647		CSN48 2 03 I03	GSM8150233		tissue:beta cells\|cell type:beta cells\|treatment:CSN48\|geo loc name:missing\|collection date:missing	CSN48 2 03 I03	bcl2fastq2 2.19.1 Alignment with GSNAP v2019 06 10 to the GRCz11 and reference and Ensembl gene annotation 95 was used to detect spiice sites gsnap.sse42 d GRCz11 gunzip A sam t 20 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 n 1 m 0.6 s EnsemblGene 95.ss.GRCz11.iit N 0 Counts were created with featureCounts v2.0.1; featureCounts a EnsemblGene 95.GRCz11.TR.gtf s 0 p o bfx1391.GRCz11.e95.tsv Q 1 T 8 Assembly: GRCz11 Supplementary files format and content: tab separated file with the output of featurecounts where each column represent either a sample or gene information start end strand geneid and each row is a gene. Cells countain fragments per gene per sample.	beta cells	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	cell type:beta cells\|treatment:CSN48	GSM8150233	GSM8150233: CSN48 2 03 I03; Danio rerio; RNA Seq	GSM8150233 r1	GSM8150233	1	The cells are sorted with an Aria III FACS into a 384 well plate pre loaded with 0.5 µl freshly prepared lysis buffer 0.2 % Tween 20 solution with 4 U/µl murine RNase inhibitor NEB. post the sort the plate is shortly centrifuged and lysed cells stored at 80°C.post thawing the plate the cells are immediately mixed with 0.5 µl of a primer mix containing 5 mM dNTP Invitrogen 0.5 µM dT primer* 2 U RNase Inhibitor NEB ERCC spike in mix with a final dilution of 1:2107. RNA is denatured for 3 minutes at 72 °C followed by reverse transcription at 42 °C for 90 min post filling up to 1.5 µl with RT buffer mix for a final concentration of 1x superscript II buffer Invitrogen 1 M betaine 5 mM DTT 6 mM MgCl2 1 µM TSO primer 2.3 U RNase Inhibitor and 25 U Superscript II. post synthesis the reverse transcriptase is inactivated at 70°C for 15 min. The cDNA is amplified using Kapa HiFi HotStart Readymix Peqlab at a final 1x concentration and 0.1 uM UPprimer under following cycling conditions: initial denaturation at 98°C for 3 min 23 cycles [98°C 20 sec 67°C 15 sec 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6x volume of hydrophobic Sera Mag SpeedBeads GE Healthcare resuspended in a buffer consisting of 10 mM Tris 20 mM EDTA 18.5 % w/v PEG 8000 and 2 M sodium chloride solution and DNA is eluted in 12 ul nuclease free water. The concentration of the samples is measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates Corning using AccuBlue Broad range chemistry Biotium For library preparation up to 700 pg cDNA maximal 2 µl is desiccated and rehydrated in 1 ul Tagmentation mix 1x TTBL buffer 0.1 ul Tagment DNA Enzyme; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme and tagmented at 55°C for 5 min. Subsequently Illumina indices are added during PCR 72°C 3 min 98°C 30 sec 13 cycles [98°C 10 sec 63°C 20 sec 72°C 1 min] 72°C 5 min with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.17 µM dual indexing primer…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495499		loader:fastq load.py	L53805_Track-95554_R1.fastq.gz L53805_Track-95554_R2.fastq.gz	fastq fastq	95352048.0	934824.0	GSM8150233 r1	0:51 1:51	A:25907556;C:20064750;G:20900153;T:28474753;N:4836	51	51	25907556	20064750	20900153	28474753	4836	SRX23964309	SRS20763949	SRA1825239	Dresden-concept Genome Center, TU Dresden	Ninov Lab, CRTD, TU Dresden	2	0.79315	0.80387	0.08817	0.09613	0.98632	0.98595	0.63242	0.63879	51	51	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Germany	2024-03-15	Undetermined	Larval	Pancreas	Endocrine System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;