metadata: run_metadata: 26 rows where devstage_curation_coarse = "Undetermined" and tissue_curation

26 rows where devstage_curation_coarse = "Undetermined" 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.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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
34324	34324	SRR31647630	SRX27010714	SRS23475005	SRP550229	PRJNA1195876	Anti Müllerian hormone signalling sustains circadian homeostasis in zebrafish [scRNA seq]	GSE283840	Transcriptome Analysis	Circadian clocks temporally orchestrate the behavioural and physiological rhythms. The core molecules establishing the circadian clock are clear; however the critical signalling pathways that cause or favour the homeostasis are poorly understood. Here we report that anti Müllerian hormone Amh mediated signalling plays an important role in sustaining circadian homeostasis in zebrafish. Remarkably amh knockout dampens molecular clock oscillations and disrupts both behavioural and hormonal circadian rhythms which were recapitulated in bmpr2a null mutants. Somatotropes and gonadotropes were identified as Amh positive pituitary cell populations. Single cell transcriptome analysis further revealed a lineage specific regulation of pituitary clock by Amh. Moreover Amh induced effect on clock gene expression could be abolished by blocking Smad1/5/9 phosphorylation and bmpr2a knockout. Mechanistically Amh binds to its receptors Bmpr2a/Bmpr1bb which in turn activate Smad1/5/9 by phosphorylation and promote circadian gene expression. Our findings reveal a key hormone signalling pathway for circadian homeostasis in zebrafish with implications for rhythmic organ functions and circadian health. Overall design: Molecular components of the circadian clock are known; however the mechanisms by which long term circadian homeostasis and oscillation are achieved throughout complex systems and anatomical regions are poorly understood. We performed CUT&Tag and single cell RNA sequencing of wildtype amh or bmpr2a knockout zebrafish pituitary to investigate the molecular mechanism by which Amh signaling sustains circadian homeostasis.		pubmed:40348785	pituitary gland Amh KO	GSM8672964	source name:pituitary gland\|tissue:pituitary gland\|genotype:knockout Amh\|geo loc name:missing\|collection date:missing	pituitary gland Amh KO	Raw sequencing data were demultiplexed and aligned to the ENSEMBL GRCz11 zebrafish transcriptome to generate feature barcode matrices using CellRanger v5.0.1 with the default parameters. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	pituitary gland		post dissection zebrafish pituitaries from WT or amh / females were washed with cold PBS or fresh Ringer’s solution for 5 10 min followed by mechanical and enzymatic dissociation in protease solution 0.25% trypsin Life Technologies 400 mg/ml collagenase D Sigma and 1 mM EDTA in PBS and incubated at 28.5 °C for 20 30 min or until full dissociation was observed. Dissociation was stopped by the addition of 6X stop solution 6 mM CaCl2 and 30% foetal bovine serum FBS in PBS. The samples were filtered with a 40 μm cell strainer centrifuged 2000 rpm 5 min 4 °C and then resuspended in 1X PBS. Single cell cDNA libraries were synthesized using 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 according to the manufacturer’s instructions.		tissue:pituitary gland\|genotype:knockout Amh	GSM8672964	GSM8672964: pituitary gland Amh KO; Danio rerio; RNA Seq	GSM8672964 r1	GSM8672964	1	post dissection zebrafish pituitaries from WT or amh / females were washed with cold PBS or fresh Ringer's solution for 5 10 min followed by mechanical and enzymatic dissociation in protease solution 0.25% trypsin Life Technologies 400 mg/ml collagenase D Sigma and 1 mM EDTA in PBS and incubated at 28.5 °C for 20 30 min or until full dissociation was observed. Dissociation was stopped by the addition of 6X stop solution 6 mM CaCl2 and 30% foetal bovine serum FBS in PBS. The samples were filtered with a 40 μm cell strainer centrifuged 2000 rpm 5 min 4 °C and then resuspended in 1X PBS. Single cell cDNA libraries were synthesized using 10X Genomics Chromium Single Cell three prime Library & Gel Bead Kit v3.1 according to the manufacturer's instructions.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP550229		Amh_KO_R1.fq.gz Amh_KO_R2.fq.gz	fastq fastq	154810080300.0	516033601.0	GSM8672964 r1	0:150 1:150	A:51891488591;C:26616629262;G:25307529846;T:50992970078;N:1462523	150	150	51891488591	26616629262	25307529846	50992970078	1462523	SRX27010714	SRS23475005	SRA2029986	Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences	Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences												T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-12-09	Undetermined	Undetermined	Pituitary Gland	Endocrine System
34325	34325	SRR31647631	SRX27010713	SRS23475006	SRP550229	PRJNA1195876	Anti Müllerian hormone signalling sustains circadian homeostasis in zebrafish [scRNA seq]	GSE283840	Transcriptome Analysis	Circadian clocks temporally orchestrate the behavioural and physiological rhythms. The core molecules establishing the circadian clock are clear; however the critical signalling pathways that cause or favour the homeostasis are poorly understood. Here we report that anti Müllerian hormone Amh mediated signalling plays an important role in sustaining circadian homeostasis in zebrafish. Remarkably amh knockout dampens molecular clock oscillations and disrupts both behavioural and hormonal circadian rhythms which were recapitulated in bmpr2a null mutants. Somatotropes and gonadotropes were identified as Amh positive pituitary cell populations. Single cell transcriptome analysis further revealed a lineage specific regulation of pituitary clock by Amh. Moreover Amh induced effect on clock gene expression could be abolished by blocking Smad1/5/9 phosphorylation and bmpr2a knockout. Mechanistically Amh binds to its receptors Bmpr2a/Bmpr1bb which in turn activate Smad1/5/9 by phosphorylation and promote circadian gene expression. Our findings reveal a key hormone signalling pathway for circadian homeostasis in zebrafish with implications for rhythmic organ functions and circadian health. Overall design: Molecular components of the circadian clock are known; however the mechanisms by which long term circadian homeostasis and oscillation are achieved throughout complex systems and anatomical regions are poorly understood. We performed CUT&Tag and single cell RNA sequencing of wildtype amh or bmpr2a knockout zebrafish pituitary to investigate the molecular mechanism by which Amh signaling sustains circadian homeostasis.		pubmed:40348785	pituitary gland WT	GSM8672963	source name:pituitary gland\|tissue:pituitary gland\|genotype:WT\|geo loc name:missing\|collection date:missing	pituitary gland WT	Raw sequencing data were demultiplexed and aligned to the ENSEMBL GRCz11 zebrafish transcriptome to generate feature barcode matrices using CellRanger v5.0.1 with the default parameters. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	pituitary gland		post dissection zebrafish pituitaries from WT or amh / females were washed with cold PBS or fresh Ringer’s solution for 5 10 min followed by mechanical and enzymatic dissociation in protease solution 0.25% trypsin Life Technologies 400 mg/ml collagenase D Sigma and 1 mM EDTA in PBS and incubated at 28.5 °C for 20 30 min or until full dissociation was observed. Dissociation was stopped by the addition of 6X stop solution 6 mM CaCl2 and 30% foetal bovine serum FBS in PBS. The samples were filtered with a 40 μm cell strainer centrifuged 2000 rpm 5 min 4 °C and then resuspended in 1X PBS. Single cell cDNA libraries were synthesized using 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 according to the manufacturer’s instructions.		tissue:pituitary gland\|genotype:WT	GSM8672963	GSM8672963: pituitary gland WT; Danio rerio; RNA Seq	GSM8672963 r1	GSM8672963	1	post dissection zebrafish pituitaries from WT or amh / females were washed with cold PBS or fresh Ringer's solution for 5 10 min followed by mechanical and enzymatic dissociation in protease solution 0.25% trypsin Life Technologies 400 mg/ml collagenase D Sigma and 1 mM EDTA in PBS and incubated at 28.5 °C for 20 30 min or until full dissociation was observed. Dissociation was stopped by the addition of 6X stop solution 6 mM CaCl2 and 30% foetal bovine serum FBS in PBS. The samples were filtered with a 40 μm cell strainer centrifuged 2000 rpm 5 min 4 °C and then resuspended in 1X PBS. Single cell cDNA libraries were synthesized using 10X Genomics Chromium Single Cell three prime Library & Gel Bead Kit v3.1 according to the manufacturer's instructions.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP550229		WT_R1.fq.gz WT_R2.fq.gz	fastq fastq	149500940700.0	498336469.0	GSM8672963 r1	0:150 1:150	A:49714239420;C:27445649314;G:26079818385;T:46259970208;N:1263373	150	150	49714239420	27445649314	26079818385	46259970208	1263373	SRX27010713	SRS23475006	SRA2029986	Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences	Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences												T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-12-09	Undetermined	Undetermined	Pituitary Gland	Endocrine System
74472	74472	SRR23824316	SRX19646193	SRS17014002	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas Ctrl replicate 2	GSM7092957	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas Ctrl replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092957	GSM7092957: Pancreas Ctrl replicate 2; Danio rerio; RNA Seq	GSM7092957 r1	GSM7092957	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	Ctrl-Pancreas-2_S8_L001_R2_001.fastq.gz Ctrl-Pancreas-2_S8_L001_R1_001.fastq.gz	fastq fastq	4689094030.0	39738085.0	GSM7092957 r1	0:28 1:90	A:1232747701;C:1087501739;G:1176854549;T:1191883874;N:106167	28	90	1232747701	1087501739	1176854549	1191883874	106167	SRX19646193	SRS17014002	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00515	0.93252	0.00155	0.06137	0.99648	0.88692	0.38705	0.60914	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74473	74473	SRR23824317	SRX19646193	SRS17014002	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas Ctrl replicate 2	GSM7092957	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas Ctrl replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092957	GSM7092957: Pancreas Ctrl replicate 2; Danio rerio; RNA Seq	GSM7092957 r1	GSM7092957	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	Ctrl-Pancreas-2_S8_L002_R2_001.fastq.gz Ctrl-Pancreas-2_S8_L002_R1_001.fastq.gz	fastq fastq	4677907984.0	39643288.0	GSM7092957 r2	0:28 1:90	A:1227626448;C:1085304810;G:1174779891;T:1190095936;N:100899	28	90	1227626448	1085304810	1174779891	1190095936	100899	SRX19646193	SRS17014002	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00531	0.93306	0.00158	0.06221	0.99596	0.88749	0.37673	0.60528	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74474	74474	SRR23824318	SRX19646193	SRS17014002	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas Ctrl replicate 2	GSM7092957	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas Ctrl replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092957	GSM7092957: Pancreas Ctrl replicate 2; Danio rerio; RNA Seq	GSM7092957 r1	GSM7092957	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	Ctrl-Pancreas-2_S8_L003_R1_001.fastq.gz Ctrl-Pancreas-2_S8_L003_R2_001.fastq.gz	fastq fastq	4761421422.0	40351029.0	GSM7092957 r3	0:28 1:90	A:1250348494;C:1104936433;G:1195812813;T:1210226243;N:97439	28	90	1250348494	1104936433	1195812813	1210226243	97439	SRX19646193	SRS17014002	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00518	0.93314	0.00149	0.06284	0.99596	0.88753	0.3933	0.60442	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74475	74475	SRR23824319	SRX19646193	SRS17014002	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas Ctrl replicate 2	GSM7092957	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas Ctrl replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092957	GSM7092957: Pancreas Ctrl replicate 2; Danio rerio; RNA Seq	GSM7092957 r1	GSM7092957	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	Ctrl-Pancreas-2_S8_L004_R2_001.fastq.gz Ctrl-Pancreas-2_S8_L004_R1_001.fastq.gz	fastq fastq	4667970850.0	39559075.0	GSM7092957 r4	0:28 1:90	A:1226515454;C:1082416982;G:1171222300;T:1187726852;N:89262	28	90	1226515454	1082416982	1171222300	1187726852	89262	SRX19646193	SRS17014002	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00499	0.93259	0.00167	0.0614	0.9959	0.88755	0.38604	0.53191	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74476	74476	SRR23824320	SRX19646192	SRS17014003	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas Ctrl replicate 1	GSM7092956	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas Ctrl replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092956	GSM7092956: Pancreas Ctrl replicate 1; Danio rerio; RNA Seq	GSM7092956 r1	GSM7092956	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	Ctrl-Pancreas-1_S4_L001_R1_001.fastq.gz Ctrl-Pancreas-1_S4_L001_R2_001.fastq.gz	fastq fastq	4087782314.0	34642223.0	GSM7092956 r1	0:28 1:90	A:988379101;C:980631744;G:1075271505;T:1043407296;N:92668	28	90	988379101	980631744	1075271505	1043407296	92668	SRX19646192	SRS17014003	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00484	0.96438	0.00131	0.03915	0.99697	0.91311	0.4152	0.60907	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74477	74477	SRR23824321	SRX19646192	SRS17014003	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas Ctrl replicate 1	GSM7092956	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas Ctrl replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092956	GSM7092956: Pancreas Ctrl replicate 1; Danio rerio; RNA Seq	GSM7092956 r1	GSM7092956	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	Ctrl-Pancreas-1_S4_L002_R1_001.fastq.gz Ctrl-Pancreas-1_S4_L002_R2_001.fastq.gz	fastq fastq	4117642214.0	34895273.0	GSM7092956 r2	0:28 1:90	A:995176406;C:987675179;G:1083314338;T:1051387356;N:88935	28	90	995176406	987675179	1083314338	1051387356	88935	SRX19646192	SRS17014003	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.0049	0.96448	0.00126	0.03869	0.99655	0.91151	0.42291	0.61172	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74478	74478	SRR23824322	SRX19646192	SRS17014003	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas Ctrl replicate 1	GSM7092956	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas Ctrl replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092956	GSM7092956: Pancreas Ctrl replicate 1; Danio rerio; RNA Seq	GSM7092956 r1	GSM7092956	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	Ctrl-Pancreas-1_S4_L003_R1_001.fastq.gz Ctrl-Pancreas-1_S4_L003_R2_001.fastq.gz	fastq fastq	4158634470.0	35242665.0	GSM7092956 r3	0:28 1:90	A:1004519785;C:998011643;G:1094510237;T:1061510107;N:82698	28	90	1004519785	998011643	1094510237	1061510107	82698	SRX19646192	SRS17014003	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00486	0.96439	0.00124	0.04007	0.99689	0.91064	0.40883	0.61125	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74479	74479	SRR23824323	SRX19646192	SRS17014003	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas Ctrl replicate 1	GSM7092956	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas Ctrl replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092956	GSM7092956: Pancreas Ctrl replicate 1; Danio rerio; RNA Seq	GSM7092956 r1	GSM7092956	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	Ctrl-Pancreas-1_S4_L004_R1_001.fastq.gz Ctrl-Pancreas-1_S4_L004_R2_001.fastq.gz	fastq fastq	4084344502.0	34613089.0	GSM7092956 r4	0:28 1:90	A:988069108;C:979213026;G:1073790783;T:1043193951;N:77634	28	90	988069108	979213026	1073790783	1043193951	77634	SRX19646192	SRS17014003	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00479	0.96445	0.00132	0.0387	0.99701	0.91086	0.42113	0.61441	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74504	74504	SRR23824344	SRX19646185	SRS17013995	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas 7 dpi replicate 1	GSM7092948	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas 7 dpi replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092948	GSM7092948: Pancreas 7 dpi replicate 1; Danio rerio; RNA Seq	GSM7092948 r1	GSM7092948	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	7dpi-Pancreas-1_S20_L001_R1_001.fastq.gz 7dpi-Pancreas-1_S20_L001_R2_001.fastq.gz	fastq fastq	4549683756.0	38556642.0	GSM7092948 r1	0:28 1:90	A:1143775236;C:1105204092;G:1203189006;T:1097413006;N:102416	28	90	1143775236	1105204092	1203189006	1097413006	102416	SRX19646185	SRS17013995	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.02063	0.94539	0.00665	0.10755	0.99622	0.91309	0.32854	0.54953	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74505	74505	SRR23824345	SRX19646185	SRS17013995	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas 7 dpi replicate 1	GSM7092948	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas 7 dpi replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092948	GSM7092948: Pancreas 7 dpi replicate 1; Danio rerio; RNA Seq	GSM7092948 r1	GSM7092948	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	7dpi-Pancreas-1_S20_L002_R1_001.fastq.gz 7dpi-Pancreas-1_S20_L002_R2_001.fastq.gz	fastq fastq	4517687938.0	38285491.0	GSM7092948 r2	0:28 1:90	A:1134622351;C:1097536764;G:1194906587;T:1090524287;N:97949	28	90	1134622351	1097536764	1194906587	1090524287	97949	SRX19646185	SRS17013995	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.02109	0.94517	0.00676	0.10863	0.99628	0.91252	0.3052	0.54958	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74506	74506	SRR23824346	SRX19646185	SRS17013995	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas 7 dpi replicate 1	GSM7092948	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas 7 dpi replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092948	GSM7092948: Pancreas 7 dpi replicate 1; Danio rerio; RNA Seq	GSM7092948 r1	GSM7092948	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	7dpi-Pancreas-1_S20_L003_R1_001.fastq.gz 7dpi-Pancreas-1_S20_L003_R2_001.fastq.gz	fastq fastq	4636317940.0	39290830.0	GSM7092948 r3	0:28 1:90	A:1163890164;C:1127297116;G:1227016473;T:1118019811;N:94376	28	90	1163890164	1127297116	1227016473	1118019811	94376	SRX19646185	SRS17013995	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.02099	0.94599	0.00695	0.10973	0.99618	0.9123	0.34518	0.51887	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74507	74507	SRR23824347	SRX19646185	SRS17013995	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas 7 dpi replicate 1	GSM7092948	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas 7 dpi replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092948	GSM7092948: Pancreas 7 dpi replicate 1; Danio rerio; RNA Seq	GSM7092948 r1	GSM7092948	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	7dpi-Pancreas-1_S20_L004_R1_001.fastq.gz 7dpi-Pancreas-1_S20_L004_R2_001.fastq.gz	fastq fastq	4497198064.0	38111848.0	GSM7092948 r4	0:28 1:90	A:1131098871;C:1091572129;G:1188115242;T:1086325472;N:86350	28	90	1131098871	1091572129	1188115242	1086325472	86350	SRX19646185	SRS17013995	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.02003	0.9465	0.00658	0.10877	0.99596	0.91171	0.34392	0.54247	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74508	74508	SRR23824348	SRX19646184	SRS17013994	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas 7 dpi replicate 2	GSM7092949	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas 7 dpi replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092949	GSM7092949: Pancreas 7 dpi replicate 2; Danio rerio; RNA Seq	GSM7092949 r1	GSM7092949	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	7dpi-Pancreas-2_S24_L001_R1_001.fastq.gz 7dpi-Pancreas-2_S24_L001_R2_001.fastq.gz	fastq fastq	3694404180.0	31308510.0	GSM7092949 r1	0:28 1:90	A:925642312;C:897963126;G:972697543;T:898017524;N:83675	28	90	925642312	897963126	972697543	898017524	83675	SRX19646184	SRS17013994	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.01944	0.9386	0.00639	0.10031	0.99561	0.90763	0.34147	0.64485	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74509	74509	SRR23824349	SRX19646184	SRS17013994	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas 7 dpi replicate 2	GSM7092949	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas 7 dpi replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092949	GSM7092949: Pancreas 7 dpi replicate 2; Danio rerio; RNA Seq	GSM7092949 r1	GSM7092949	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	7dpi-Pancreas-2_S24_L002_R1_001.fastq.gz 7dpi-Pancreas-2_S24_L002_R2_001.fastq.gz	fastq fastq	3695460280.0	31317460.0	GSM7092949 r2	0:28 1:90	A:924776645;C:898527265;G:973466829;T:898610296;N:79245	28	90	924776645	898527265	973466829	898610296	79245	SRX19646184	SRS17013994	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.01959	0.93749	0.00645	0.10075	0.99571	0.90889	0.36214	0.64826	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74510	74510	SRR23824350	SRX19646184	SRS17013994	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas 7 dpi replicate 2	GSM7092949	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas 7 dpi replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092949	GSM7092949: Pancreas 7 dpi replicate 2; Danio rerio; RNA Seq	GSM7092949 r1	GSM7092949	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	7dpi-Pancreas-2_S24_L003_R1_001.fastq.gz 7dpi-Pancreas-2_S24_L003_R2_001.fastq.gz	fastq fastq	3765831586.0	31913827.0	GSM7092949 r3	0:28 1:90	A:942337142;C:916041305;G:992299130;T:915077569;N:76440	28	90	942337142	916041305	992299130	915077569	76440	SRX19646184	SRS17013994	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.0193	0.93865	0.00649	0.1012	0.99614	0.9093	0.34282	0.63758	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74511	74511	SRR23824351	SRX19646184	SRS17013994	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas 7 dpi replicate 2	GSM7092949	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas 7 dpi replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092949	GSM7092949: Pancreas 7 dpi replicate 2; Danio rerio; RNA Seq	GSM7092949 r1	GSM7092949	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	7dpi-Pancreas-2_S24_L004_R1_001.fastq.gz 7dpi-Pancreas-2_S24_L004_R2_001.fastq.gz	fastq fastq	3665890896.0	31066872.0	GSM7092949 r4	0:28 1:90	A:918497729;C:890554002;G:964737735;T:892032221;N:69209	28	90	918497729	890554002	964737735	892032221	69209	SRX19646184	SRS17013994	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.01901	0.93844	0.0062	0.10108	0.99592	0.90796	0.32691	0.64748	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74544	74544	SRR23824380	SRX19646175	SRS17013985	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas 1 dpi replicate 2	GSM7092941	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas 1 dpi replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092941	GSM7092941: Pancreas 1 dpi replicate 2; Danio rerio; RNA Seq	GSM7092941 r1	GSM7092941	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	1dpi-Pancreas-2_S16_L001_R1_001.fastq.gz 1dpi-Pancreas-2_S16_L001_R2_001.fastq.gz	fastq fastq	4309260644.0	36519158.0	GSM7092941 r1	0:28 1:90	A:1046247537;C:1048122611;G:1162975668;T:1051816689;N:98139	28	90	1046247537	1048122611	1162975668	1051816689	98139	SRX19646175	SRS17013985	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00671	0.9366	0.00224	0.09388	0.99651	0.90189	0.37644	0.63945	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74545	74545	SRR23824381	SRX19646175	SRS17013985	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas 1 dpi replicate 2	GSM7092941	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas 1 dpi replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092941	GSM7092941: Pancreas 1 dpi replicate 2; Danio rerio; RNA Seq	GSM7092941 r1	GSM7092941	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	1dpi-Pancreas-2_S16_L002_R1_001.fastq.gz 1dpi-Pancreas-2_S16_L002_R2_001.fastq.gz	fastq fastq	4297639414.0	36420673.0	GSM7092941 r2	0:28 1:90	A:1043016765;C:1045256212;G:1159666945;T:1049606913;N:92579	28	90	1043016765	1045256212	1159666945	1049606913	92579	SRX19646175	SRS17013985	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00646	0.93715	0.00204	0.09343	0.99685	0.90327	0.38255	0.63012	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74546	74546	SRR23824382	SRX19646175	SRS17013985	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas 1 dpi replicate 2	GSM7092941	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas 1 dpi replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092941	GSM7092941: Pancreas 1 dpi replicate 2; Danio rerio; RNA Seq	GSM7092941 r1	GSM7092941	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	1dpi-Pancreas-2_S16_L003_R1_001.fastq.gz 1dpi-Pancreas-2_S16_L003_R2_001.fastq.gz	fastq fastq	4389542888.0	37199516.0	GSM7092941 r3	0:28 1:90	A:1064162384;C:1068512248;G:1185538637;T:1071241453;N:88166	28	90	1064162384	1068512248	1185538637	1071241453	88166	SRX19646175	SRS17013985	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00644	0.93752	0.0021	0.09439	0.99659	0.90382	0.37098	0.63183	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74547	74547	SRR23824383	SRX19646175	SRS17013985	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas 1 dpi replicate 2	GSM7092941	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas 1 dpi replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092941	GSM7092941: Pancreas 1 dpi replicate 2; Danio rerio; RNA Seq	GSM7092941 r1	GSM7092941	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	1dpi-Pancreas-2_S16_L004_R1_001.fastq.gz 1dpi-Pancreas-2_S16_L004_R2_001.fastq.gz	fastq fastq	4277274856.0	36248092.0	GSM7092941 r4	0:28 1:90	A:1039365242;C:1039483839;G:1153145758;T:1045198402;N:81615	28	90	1039365242	1039483839	1153145758	1045198402	81615	SRX19646175	SRS17013985	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00627	0.93724	0.00211	0.09386	0.99659	0.90262	0.4275	0.61845	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74548	74548	SRR23824388	SRX19646174	SRS17013984	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas 1 dpi replicate 1	GSM7092940	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas 1 dpi replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092940	GSM7092940: Pancreas 1 dpi replicate 1; Danio rerio; RNA Seq	GSM7092940 r1	GSM7092940	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	1dpi-Pancreas-1_S12_L001_R1_001.fastq.gz 1dpi-Pancreas-1_S12_L001_R2_001.fastq.gz	fastq fastq	5429558190.0	46013205.0	GSM7092940 r1	0:28 1:90	A:1303586809;C:1328725175;G:1505666398;T:1291455764;N:124044	28	90	1303586809	1328725175	1505666398	1291455764	124044	SRX19646174	SRS17013984	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00632	0.94424	0.00213	0.10919	0.99695	0.91936	0.36162	0.55183	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74549	74549	SRR23824389	SRX19646174	SRS17013984	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas 1 dpi replicate 1	GSM7092940	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas 1 dpi replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092940	GSM7092940: Pancreas 1 dpi replicate 1; Danio rerio; RNA Seq	GSM7092940 r1	GSM7092940	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	1dpi-Pancreas-1_S12_L002_R1_001.fastq.gz 1dpi-Pancreas-1_S12_L002_R2_001.fastq.gz	fastq fastq	5406650142.0	45819069.0	GSM7092940 r2	0:28 1:90	A:1297924443;C:1322864150;G:1498812275;T:1286932180;N:117094	28	90	1297924443	1322864150	1498812275	1286932180	117094	SRX19646174	SRS17013984	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00647	0.94374	0.00235	0.11112	0.99699	0.91816	0.3583	0.56118	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74550	74550	SRR23824390	SRX19646174	SRS17013984	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas 1 dpi replicate 1	GSM7092940	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas 1 dpi replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092940	GSM7092940: Pancreas 1 dpi replicate 1; Danio rerio; RNA Seq	GSM7092940 r1	GSM7092940	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	1dpi-Pancreas-1_S12_L003_R1_001.fastq.gz 1dpi-Pancreas-1_S12_L003_R2_001.fastq.gz	fastq fastq	5529750810.0	46862295.0	GSM7092940 r3	0:28 1:90	A:1325091638;C:1354598961;G:1534908275;T:1315039358;N:112578	28	90	1325091638	1354598961	1534908275	1315039358	112578	SRX19646174	SRS17013984	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00611	0.94576	0.00203	0.11108	0.99709	0.91863	0.38685	0.65557	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Pancreas	Endocrine System
74551	74551	SRR23824391	SRX19646174	SRS17013984	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536	Pancreas 1 dpi replicate 1	GSM7092940	source name:Pancreas\|tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	Pancreas 1 dpi replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Pancreas	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Pancreas\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092940	GSM7092940: Pancreas 1 dpi replicate 1; Danio rerio; RNA Seq	GSM7092940 r1	GSM7092940	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	1dpi-Pancreas-1_S12_L004_R1_001.fastq.gz 1dpi-Pancreas-1_S12_L004_R2_001.fastq.gz	fastq fastq	5383384318.0	45621901.0	GSM7092940 r4	0:28 1:90	A:1294350602;C:1316150189;G:1490887301;T:1281893201;N:103025	28	90	1294350602	1316150189	1490887301	1281893201	103025	SRX19646174	SRS17013984	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00616	0.94398	0.00206	0.10993	0.99715	0.91963	0.37232	0.65892	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	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");;