rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
28482,SRR26266492,SRX21975998,SRS19051834,SRP464334,PRJNA1023540,ABCA7 dependent induction of neuropeptide Y is required for synaptic resilience in Alzheimer's disease through BDNF/NGFR signaling,GSE244550,Transcriptome Analysis,Genetic variants in ABCA7  an Alzheimer's disease AD associated gene  elevate AD risk  yet its functional relevance to the etiology is unclear. We generated a CRISPR Cas9 mediated abca7 knockout zebrafish to explore ABCA7's role in AD. Single cell transcriptomics in heterozygous abca7+/  knockout combined with Aß42 toxicity revealed that ABCA7 is crucial for neuropeptide Y NPY  brain derived neurotrophic factor BDNF  and nerve growth factor receptor NGFR expressions  which are crucial for synaptic integrity  astroglial proliferation  and microglial prevalence. Impaired NPY induction decreased BDNF and synaptic density  which are rescuable with ectopic NPY. In induced pluripotent stem cell derived human neurons exposed to Aß42  ABCA7 /  suppresses NPY. Clinical data showed reduced NPY in AD correlated with elevated Braak stages  genetic variants in NPY associated with AD  and epigenetic changes in NPY  NGFR  and BDNF promoters linked to ABCA7 variants. Therefore  ABCA7 dependent NPY signaling via BDNF NGFR maintains synaptic integrity  implicating its impairment in increased AD risk through reduced brain resilience. Overall design: WT and abca7+/  zebrafish injected with Amyloid beta 42 peptide as described Bhatatrai et al. 2016 and cells were dissociated  sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads were aligned to zebrafish genome GRChZ 11  v 105 was used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data,,pubmed:39216475,,telencephalon  abca7 k/o   Ab42 injected,GSM7819018,,source name:telencephalon|tissue:telencephalon|genotype:abca7 +/ |treatment:Ab42|geo loc name:missing|collection date:missing,telencephalon  abca7 k/o   Ab42 injected,The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genomics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger,telencephalon,WT AB and abca7 +/  knock out lines were injected with Amyloid beta 42 peptide  and PBS as control as descibed Bhatatrai et al. 2016.,Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH7.5  at 28°C ±1°C in groups of 20 animals per 2.8L.,tissue:telencephalon|genotype:abca7 +/ |treatment:Ab42,GSM7819018,GSM7819018: telencephalon  abca7 k/o   Ab42 injected; Danio rerio; RNA Seq,GSM7819018 r1,GSM7819018,1,Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP464334,,loader:fastq load.py,CP021_S12_L001_I1_001.fastq.gz CP021_S12_L001_I2_001.fastq.gz CP021_S12_L001_R1_001.fastq.gz CP021_S12_L001_R2_001.fastq.gz,fastq fastq fastq fastq,46637839920.0,210080360.0,GSM7819018 r1,0:10 1:10 2:101 3:101,A:12160340644;C:7050177030;G:7302497483;T:15922643298;N:574265,10,10,101,101,12160340644,7050177030,7302497483,15922643298,574265,SRX21975998,SRS19051834,SRA1725563,"Neurology & TAUB Institute, Columbia University","Neurology & TAUB Institute, Columbia University",2,0.00333,0.89749,0.00051,0.26345,0.99821,0.73539,0.54736,0.5015,101,101,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-03,Undetermined,Undetermined,Brain,Nervous System
28483,SRR26266493,SRX21975998,SRS19051834,SRP464334,PRJNA1023540,ABCA7 dependent induction of neuropeptide Y is required for synaptic resilience in Alzheimer's disease through BDNF/NGFR signaling,GSE244550,Transcriptome Analysis,Genetic variants in ABCA7  an Alzheimer's disease AD associated gene  elevate AD risk  yet its functional relevance to the etiology is unclear. We generated a CRISPR Cas9 mediated abca7 knockout zebrafish to explore ABCA7's role in AD. Single cell transcriptomics in heterozygous abca7+/  knockout combined with Aß42 toxicity revealed that ABCA7 is crucial for neuropeptide Y NPY  brain derived neurotrophic factor BDNF  and nerve growth factor receptor NGFR expressions  which are crucial for synaptic integrity  astroglial proliferation  and microglial prevalence. Impaired NPY induction decreased BDNF and synaptic density  which are rescuable with ectopic NPY. In induced pluripotent stem cell derived human neurons exposed to Aß42  ABCA7 /  suppresses NPY. Clinical data showed reduced NPY in AD correlated with elevated Braak stages  genetic variants in NPY associated with AD  and epigenetic changes in NPY  NGFR  and BDNF promoters linked to ABCA7 variants. Therefore  ABCA7 dependent NPY signaling via BDNF NGFR maintains synaptic integrity  implicating its impairment in increased AD risk through reduced brain resilience. Overall design: WT and abca7+/  zebrafish injected with Amyloid beta 42 peptide as described Bhatatrai et al. 2016 and cells were dissociated  sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads were aligned to zebrafish genome GRChZ 11  v 105 was used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data,,pubmed:39216475,,telencephalon  abca7 k/o   Ab42 injected,GSM7819018,,source name:telencephalon|tissue:telencephalon|genotype:abca7 +/ |treatment:Ab42|geo loc name:missing|collection date:missing,telencephalon  abca7 k/o   Ab42 injected,The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genomics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger,telencephalon,WT AB and abca7 +/  knock out lines were injected with Amyloid beta 42 peptide  and PBS as control as descibed Bhatatrai et al. 2016.,Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH7.5  at 28°C ±1°C in groups of 20 animals per 2.8L.,tissue:telencephalon|genotype:abca7 +/ |treatment:Ab42,GSM7819018,GSM7819018: telencephalon  abca7 k/o   Ab42 injected; Danio rerio; RNA Seq,GSM7819018 r1,GSM7819018,1,Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP464334,,loader:fastq load.py,CP021_S12_L002_I1_001.fastq.gz CP021_S12_L002_I2_001.fastq.gz CP021_S12_L002_R1_001.fastq.gz CP021_S12_L002_R2_001.fastq.gz,fastq fastq fastq fastq,47673315186.0,214744663.0,GSM7819018 r2,0:10 1:10 2:101 3:101,A:12499321052;C:7231866994;G:7443419880;T:16203206561;N:607439,10,10,101,101,12499321052,7231866994,7443419880,16203206561,607439,SRX21975998,SRS19051834,SRA1725563,"Neurology & TAUB Institute, Columbia University","Neurology & TAUB Institute, Columbia University",2,0.00305,0.89832,0.00064,0.26179,0.99851,0.73434,0.53932,0.50016,101,101,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-03,Undetermined,Undetermined,Brain,Nervous System
28484,SRR26266494,SRX21975997,SRS19051833,SRP464334,PRJNA1023540,ABCA7 dependent induction of neuropeptide Y is required for synaptic resilience in Alzheimer's disease through BDNF/NGFR signaling,GSE244550,Transcriptome Analysis,Genetic variants in ABCA7  an Alzheimer's disease AD associated gene  elevate AD risk  yet its functional relevance to the etiology is unclear. We generated a CRISPR Cas9 mediated abca7 knockout zebrafish to explore ABCA7's role in AD. Single cell transcriptomics in heterozygous abca7+/  knockout combined with Aß42 toxicity revealed that ABCA7 is crucial for neuropeptide Y NPY  brain derived neurotrophic factor BDNF  and nerve growth factor receptor NGFR expressions  which are crucial for synaptic integrity  astroglial proliferation  and microglial prevalence. Impaired NPY induction decreased BDNF and synaptic density  which are rescuable with ectopic NPY. In induced pluripotent stem cell derived human neurons exposed to Aß42  ABCA7 /  suppresses NPY. Clinical data showed reduced NPY in AD correlated with elevated Braak stages  genetic variants in NPY associated with AD  and epigenetic changes in NPY  NGFR  and BDNF promoters linked to ABCA7 variants. Therefore  ABCA7 dependent NPY signaling via BDNF NGFR maintains synaptic integrity  implicating its impairment in increased AD risk through reduced brain resilience. Overall design: WT and abca7+/  zebrafish injected with Amyloid beta 42 peptide as described Bhatatrai et al. 2016 and cells were dissociated  sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads were aligned to zebrafish genome GRChZ 11  v 105 was used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data,,pubmed:39216475,,telencephalon  abca7 k/o   PBS injected,GSM7819017,,source name:telencephalon|tissue:telencephalon|genotype:abca7 +/ |treatment:PBS|geo loc name:missing|collection date:missing,telencephalon  abca7 k/o   PBS injected,The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genomics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger,telencephalon,WT AB and abca7 +/  knock out lines were injected with Amyloid beta 42 peptide  and PBS as control as descibed Bhatatrai et al. 2016.,Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH7.5  at 28°C ±1°C in groups of 20 animals per 2.8L.,tissue:telencephalon|genotype:abca7 +/ |treatment:PBS,GSM7819017,GSM7819017: telencephalon  abca7 k/o   PBS injected; Danio rerio; RNA Seq,GSM7819017 r1,GSM7819017,1,Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP464334,,loader:fastq load.py,CP020_S11_L001_I1_001.fastq.gz CP020_S11_L001_I2_001.fastq.gz CP020_S11_L001_R1_001.fastq.gz CP020_S11_L001_R2_001.fastq.gz,fastq fastq fastq fastq,45135900918.0,203314869.0,GSM7819017 r1,0:10 1:10 2:101 3:101,A:11807801920;C:6876592307;G:7115059785;T:15269592915;N:556611,10,10,101,101,11807801920,6876592307,7115059785,15269592915,556611,SRX21975997,SRS19051833,SRA1725563,"Neurology & TAUB Institute, Columbia University","Neurology & TAUB Institute, Columbia University",2,0.00293,0.90111,0.00093,0.28713,0.99882,0.73687,0.58461,0.50013,101,101,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-03,Undetermined,Undetermined,Brain,Nervous System
28485,SRR26266495,SRX21975997,SRS19051833,SRP464334,PRJNA1023540,ABCA7 dependent induction of neuropeptide Y is required for synaptic resilience in Alzheimer's disease through BDNF/NGFR signaling,GSE244550,Transcriptome Analysis,Genetic variants in ABCA7  an Alzheimer's disease AD associated gene  elevate AD risk  yet its functional relevance to the etiology is unclear. We generated a CRISPR Cas9 mediated abca7 knockout zebrafish to explore ABCA7's role in AD. Single cell transcriptomics in heterozygous abca7+/  knockout combined with Aß42 toxicity revealed that ABCA7 is crucial for neuropeptide Y NPY  brain derived neurotrophic factor BDNF  and nerve growth factor receptor NGFR expressions  which are crucial for synaptic integrity  astroglial proliferation  and microglial prevalence. Impaired NPY induction decreased BDNF and synaptic density  which are rescuable with ectopic NPY. In induced pluripotent stem cell derived human neurons exposed to Aß42  ABCA7 /  suppresses NPY. Clinical data showed reduced NPY in AD correlated with elevated Braak stages  genetic variants in NPY associated with AD  and epigenetic changes in NPY  NGFR  and BDNF promoters linked to ABCA7 variants. Therefore  ABCA7 dependent NPY signaling via BDNF NGFR maintains synaptic integrity  implicating its impairment in increased AD risk through reduced brain resilience. Overall design: WT and abca7+/  zebrafish injected with Amyloid beta 42 peptide as described Bhatatrai et al. 2016 and cells were dissociated  sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads were aligned to zebrafish genome GRChZ 11  v 105 was used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data,,pubmed:39216475,,telencephalon  abca7 k/o   PBS injected,GSM7819017,,source name:telencephalon|tissue:telencephalon|genotype:abca7 +/ |treatment:PBS|geo loc name:missing|collection date:missing,telencephalon  abca7 k/o   PBS injected,The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genomics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger,telencephalon,WT AB and abca7 +/  knock out lines were injected with Amyloid beta 42 peptide  and PBS as control as descibed Bhatatrai et al. 2016.,Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH7.5  at 28°C ±1°C in groups of 20 animals per 2.8L.,tissue:telencephalon|genotype:abca7 +/ |treatment:PBS,GSM7819017,GSM7819017: telencephalon  abca7 k/o   PBS injected; Danio rerio; RNA Seq,GSM7819017 r1,GSM7819017,1,Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP464334,,loader:fastq load.py,CP020_S11_L002_I1_001.fastq.gz CP020_S11_L002_I2_001.fastq.gz CP020_S11_L002_R1_001.fastq.gz CP020_S11_L002_R2_001.fastq.gz,fastq fastq fastq fastq,46689428280.0,210312740.0,GSM7819017 r2,0:10 1:10 2:101 3:101,A:12281435026;C:7136662243;G:7338982062;T:15725501987;N:592162,10,10,101,101,12281435026,7136662243,7338982062,15725501987,592162,SRX21975997,SRS19051833,SRA1725563,"Neurology & TAUB Institute, Columbia University","Neurology & TAUB Institute, Columbia University",2,0.00317,0.90041,0.00069,0.28878,0.99819,0.73657,0.60869,0.49401,101,101,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-03,Undetermined,Undetermined,Brain,Nervous System
28486,SRR26266496,SRX21975996,SRS19051832,SRP464334,PRJNA1023540,ABCA7 dependent induction of neuropeptide Y is required for synaptic resilience in Alzheimer's disease through BDNF/NGFR signaling,GSE244550,Transcriptome Analysis,Genetic variants in ABCA7  an Alzheimer's disease AD associated gene  elevate AD risk  yet its functional relevance to the etiology is unclear. We generated a CRISPR Cas9 mediated abca7 knockout zebrafish to explore ABCA7's role in AD. Single cell transcriptomics in heterozygous abca7+/  knockout combined with Aß42 toxicity revealed that ABCA7 is crucial for neuropeptide Y NPY  brain derived neurotrophic factor BDNF  and nerve growth factor receptor NGFR expressions  which are crucial for synaptic integrity  astroglial proliferation  and microglial prevalence. Impaired NPY induction decreased BDNF and synaptic density  which are rescuable with ectopic NPY. In induced pluripotent stem cell derived human neurons exposed to Aß42  ABCA7 /  suppresses NPY. Clinical data showed reduced NPY in AD correlated with elevated Braak stages  genetic variants in NPY associated with AD  and epigenetic changes in NPY  NGFR  and BDNF promoters linked to ABCA7 variants. Therefore  ABCA7 dependent NPY signaling via BDNF NGFR maintains synaptic integrity  implicating its impairment in increased AD risk through reduced brain resilience. Overall design: WT and abca7+/  zebrafish injected with Amyloid beta 42 peptide as described Bhatatrai et al. 2016 and cells were dissociated  sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads were aligned to zebrafish genome GRChZ 11  v 105 was used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data,,pubmed:39216475,,telencephalon  WT Ab42 injected,GSM7819016,,source name:telencephalon|tissue:telencephalon|genotype:WT AB|treatment:Ab42|geo loc name:missing|collection date:missing,telencephalon  WT Ab42 injected,The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genomics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger,telencephalon,WT AB and abca7 +/  knock out lines were injected with Amyloid beta 42 peptide  and PBS as control as descibed Bhatatrai et al. 2016.,Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH7.5  at 28°C ±1°C in groups of 20 animals per 2.8L.,tissue:telencephalon|genotype:WT AB|treatment:Ab42,GSM7819016,GSM7819016: telencephalon  WT Ab42 injected; Danio rerio; RNA Seq,GSM7819016 r1,GSM7819016,1,Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP464334,,loader:fastq load.py,CP019_S10_L001_I1_001.fastq.gz CP019_S10_L001_I2_001.fastq.gz CP019_S10_L001_R1_001.fastq.gz CP019_S10_L001_R2_001.fastq.gz,fastq fastq fastq fastq,48132368784.0,216812472.0,GSM7819016 r1,0:10 1:10 2:101 3:101,A:12479944041;C:7377568938;G:7622029272;T:16315981376;N:595717,10,10,101,101,12479944041,7377568938,7622029272,16315981376,595717,SRX21975996,SRS19051832,SRA1725563,"Neurology & TAUB Institute, Columbia University","Neurology & TAUB Institute, Columbia University",2,0.00237,0.90638,0.00049,0.23035,0.99876,0.73612,0.50793,0.50292,101,101,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-03,Undetermined,Undetermined,Brain,Nervous System
28487,SRR26266497,SRX21975996,SRS19051832,SRP464334,PRJNA1023540,ABCA7 dependent induction of neuropeptide Y is required for synaptic resilience in Alzheimer's disease through BDNF/NGFR signaling,GSE244550,Transcriptome Analysis,Genetic variants in ABCA7  an Alzheimer's disease AD associated gene  elevate AD risk  yet its functional relevance to the etiology is unclear. We generated a CRISPR Cas9 mediated abca7 knockout zebrafish to explore ABCA7's role in AD. Single cell transcriptomics in heterozygous abca7+/  knockout combined with Aß42 toxicity revealed that ABCA7 is crucial for neuropeptide Y NPY  brain derived neurotrophic factor BDNF  and nerve growth factor receptor NGFR expressions  which are crucial for synaptic integrity  astroglial proliferation  and microglial prevalence. Impaired NPY induction decreased BDNF and synaptic density  which are rescuable with ectopic NPY. In induced pluripotent stem cell derived human neurons exposed to Aß42  ABCA7 /  suppresses NPY. Clinical data showed reduced NPY in AD correlated with elevated Braak stages  genetic variants in NPY associated with AD  and epigenetic changes in NPY  NGFR  and BDNF promoters linked to ABCA7 variants. Therefore  ABCA7 dependent NPY signaling via BDNF NGFR maintains synaptic integrity  implicating its impairment in increased AD risk through reduced brain resilience. Overall design: WT and abca7+/  zebrafish injected with Amyloid beta 42 peptide as described Bhatatrai et al. 2016 and cells were dissociated  sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads were aligned to zebrafish genome GRChZ 11  v 105 was used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data,,pubmed:39216475,,telencephalon  WT Ab42 injected,GSM7819016,,source name:telencephalon|tissue:telencephalon|genotype:WT AB|treatment:Ab42|geo loc name:missing|collection date:missing,telencephalon  WT Ab42 injected,The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genomics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger,telencephalon,WT AB and abca7 +/  knock out lines were injected with Amyloid beta 42 peptide  and PBS as control as descibed Bhatatrai et al. 2016.,Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH7.5  at 28°C ±1°C in groups of 20 animals per 2.8L.,tissue:telencephalon|genotype:WT AB|treatment:Ab42,GSM7819016,GSM7819016: telencephalon  WT Ab42 injected; Danio rerio; RNA Seq,GSM7819016 r1,GSM7819016,1,Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP464334,,loader:fastq load.py,CP019_S10_L002_I1_001.fastq.gz CP019_S10_L002_I2_001.fastq.gz CP019_S10_L002_R1_001.fastq.gz CP019_S10_L002_R2_001.fastq.gz,fastq fastq fastq fastq,49675882836.0,223765238.0,GSM7819016 r2,0:10 1:10 2:101 3:101,A:12950211284;C:7640502677;G:7844712651;T:16764526831;N:624633,10,10,101,101,12950211284,7640502677,7844712651,16764526831,624633,SRX21975996,SRS19051832,SRA1725563,"Neurology & TAUB Institute, Columbia University","Neurology & TAUB Institute, Columbia University",2,0.0034,0.9058,0.00062,0.22634,0.99825,0.73423,0.45714,0.49934,101,101,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-03,Undetermined,Undetermined,Brain,Nervous System
28488,SRR26266498,SRX21975995,SRS19051831,SRP464334,PRJNA1023540,ABCA7 dependent induction of neuropeptide Y is required for synaptic resilience in Alzheimer's disease through BDNF/NGFR signaling,GSE244550,Transcriptome Analysis,Genetic variants in ABCA7  an Alzheimer's disease AD associated gene  elevate AD risk  yet its functional relevance to the etiology is unclear. We generated a CRISPR Cas9 mediated abca7 knockout zebrafish to explore ABCA7's role in AD. Single cell transcriptomics in heterozygous abca7+/  knockout combined with Aß42 toxicity revealed that ABCA7 is crucial for neuropeptide Y NPY  brain derived neurotrophic factor BDNF  and nerve growth factor receptor NGFR expressions  which are crucial for synaptic integrity  astroglial proliferation  and microglial prevalence. Impaired NPY induction decreased BDNF and synaptic density  which are rescuable with ectopic NPY. In induced pluripotent stem cell derived human neurons exposed to Aß42  ABCA7 /  suppresses NPY. Clinical data showed reduced NPY in AD correlated with elevated Braak stages  genetic variants in NPY associated with AD  and epigenetic changes in NPY  NGFR  and BDNF promoters linked to ABCA7 variants. Therefore  ABCA7 dependent NPY signaling via BDNF NGFR maintains synaptic integrity  implicating its impairment in increased AD risk through reduced brain resilience. Overall design: WT and abca7+/  zebrafish injected with Amyloid beta 42 peptide as described Bhatatrai et al. 2016 and cells were dissociated  sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads were aligned to zebrafish genome GRChZ 11  v 105 was used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data,,pubmed:39216475,,telencephalon  WT  PBS injected,GSM7819015,,source name:telencephalon|tissue:telencephalon|genotype:WT AB|treatment:PBS|geo loc name:missing|collection date:missing,telencephalon  WT  PBS injected,The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genomics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger,telencephalon,WT AB and abca7 +/  knock out lines were injected with Amyloid beta 42 peptide  and PBS as control as descibed Bhatatrai et al. 2016.,Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH7.5  at 28°C ±1°C in groups of 20 animals per 2.8L.,tissue:telencephalon|genotype:WT AB|treatment:PBS,GSM7819015,GSM7819015: telencephalon  WT  PBS injected; Danio rerio; RNA Seq,GSM7819015 r1,GSM7819015,1,Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP464334,,loader:fastq load.py,CP018_S9_L001_I1_001.fastq.gz CP018_S9_L001_I2_001.fastq.gz CP018_S9_L001_R1_001.fastq.gz CP018_S9_L001_R2_001.fastq.gz,fastq fastq fastq fastq,45948585420.0,206975610.0,GSM7819015 r1,0:10 1:10 2:101 3:101,A:12050390597;C:6986598890;G:7200535422;T:15570981408;N:566903,10,10,101,101,12050390597,6986598890,7200535422,15570981408,566903,SRX21975995,SRS19051831,SRA1725563,"Neurology & TAUB Institute, Columbia University","Neurology & TAUB Institute, Columbia University",2,0.00353,0.89238,0.00096,0.30364,0.99841,0.73456,0.59523,0.49758,101,101,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-03,Undetermined,Undetermined,Brain,Nervous System
28489,SRR26266499,SRX21975995,SRS19051831,SRP464334,PRJNA1023540,ABCA7 dependent induction of neuropeptide Y is required for synaptic resilience in Alzheimer's disease through BDNF/NGFR signaling,GSE244550,Transcriptome Analysis,Genetic variants in ABCA7  an Alzheimer's disease AD associated gene  elevate AD risk  yet its functional relevance to the etiology is unclear. We generated a CRISPR Cas9 mediated abca7 knockout zebrafish to explore ABCA7's role in AD. Single cell transcriptomics in heterozygous abca7+/  knockout combined with Aß42 toxicity revealed that ABCA7 is crucial for neuropeptide Y NPY  brain derived neurotrophic factor BDNF  and nerve growth factor receptor NGFR expressions  which are crucial for synaptic integrity  astroglial proliferation  and microglial prevalence. Impaired NPY induction decreased BDNF and synaptic density  which are rescuable with ectopic NPY. In induced pluripotent stem cell derived human neurons exposed to Aß42  ABCA7 /  suppresses NPY. Clinical data showed reduced NPY in AD correlated with elevated Braak stages  genetic variants in NPY associated with AD  and epigenetic changes in NPY  NGFR  and BDNF promoters linked to ABCA7 variants. Therefore  ABCA7 dependent NPY signaling via BDNF NGFR maintains synaptic integrity  implicating its impairment in increased AD risk through reduced brain resilience. Overall design: WT and abca7+/  zebrafish injected with Amyloid beta 42 peptide as described Bhatatrai et al. 2016 and cells were dissociated  sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads were aligned to zebrafish genome GRChZ 11  v 105 was used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data,,pubmed:39216475,,telencephalon  WT  PBS injected,GSM7819015,,source name:telencephalon|tissue:telencephalon|genotype:WT AB|treatment:PBS|geo loc name:missing|collection date:missing,telencephalon  WT  PBS injected,The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genomics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger,telencephalon,WT AB and abca7 +/  knock out lines were injected with Amyloid beta 42 peptide  and PBS as control as descibed Bhatatrai et al. 2016.,Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH7.5  at 28°C ±1°C in groups of 20 animals per 2.8L.,tissue:telencephalon|genotype:WT AB|treatment:PBS,GSM7819015,GSM7819015: telencephalon  WT  PBS injected; Danio rerio; RNA Seq,GSM7819015 r1,GSM7819015,1,Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP464334,,loader:fastq load.py,CP018_S9_L002_I1_001.fastq.gz CP018_S9_L002_I2_001.fastq.gz CP018_S9_L002_R1_001.fastq.gz CP018_S9_L002_R2_001.fastq.gz,fastq fastq fastq fastq,47434063566.0,213666953.0,GSM7819015 r2,0:10 1:10 2:101 3:101,A:12506355665;C:7237420299;G:7414157832;T:16002190524;N:600186,10,10,101,101,12506355665,7237420299,7414157832,16002190524,600186,SRX21975995,SRS19051831,SRA1725563,"Neurology & TAUB Institute, Columbia University","Neurology & TAUB Institute, Columbia University",2,0.00327,0.8932,0.00092,0.30198,0.99831,0.73401,0.53488,0.50008,101,101,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-03,Undetermined,Undetermined,Brain,Nervous System
28707,SRR26588119,SRX22289209,SRS19340293,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 5.8 mm,GSM7871949,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871949,GSM7871949: WT 5.8 mm; Danio rerio; RNA Seq,GSM7871949 r1,GSM7871949,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0628_S3_L001_R2_001.fastq.gz FS_WT0628_S3_L001_R1_001.fastq.gz FS_WT0628_S3_L001_I1_001.fastq.gz,fastq fastq fastq,3515731348.0,27682924.0,GSM7871949 r1,0:8 1:28 2:91,A:723968955;C:551528974;G:650193733;T:593113624;N:340798,8,28,91,,723968955,551528974,650193733,593113624,340798,SRX22289209,SRS19340293,SRA1742079,Boston University,Boston University,1,0.8674,,0.17534,,0.84098,,0.62971,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28708,SRR26588120,SRX22289209,SRS19340293,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 5.8 mm,GSM7871949,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871949,GSM7871949: WT 5.8 mm; Danio rerio; RNA Seq,GSM7871949 r1,GSM7871949,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0628_S3_L002_R2_001.fastq.gz FS_WT0628_S3_L002_R1_001.fastq.gz FS_WT0628_S3_L002_I1_001.fastq.gz,fastq fastq fastq,3453128095.0,27189985.0,GSM7871949 r2,0:8 1:28 2:91,A:711376907;C:541911169;G:638181451;T:582510928;N:308180,8,28,91,,711376907,541911169,638181451,582510928,308180,SRX22289209,SRS19340293,SRA1742079,Boston University,Boston University,1,0.86684,,0.17663,,0.84108,,0.64294,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28709,SRR26588121,SRX22289209,SRS19340293,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 5.8 mm,GSM7871949,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871949,GSM7871949: WT 5.8 mm; Danio rerio; RNA Seq,GSM7871949 r1,GSM7871949,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0628_S3_L003_R2_001.fastq.gz FS_WT0628_S3_L003_R1_001.fastq.gz FS_WT0628_S3_L003_I1_001.fastq.gz,fastq fastq fastq,3525654366.0,27761058.0,GSM7871949 r3,0:8 1:28 2:91,A:725811733;C:554304351;G:651619754;T:593988032;N:532408,8,28,91,,725811733,554304351,651619754,593988032,532408,SRX22289209,SRS19340293,SRA1742079,Boston University,Boston University,1,0.86621,,0.17459,,0.83936,,0.63657,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28710,SRR26588122,SRX22289209,SRS19340293,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 5.8 mm,GSM7871949,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871949,GSM7871949: WT 5.8 mm; Danio rerio; RNA Seq,GSM7871949 r1,GSM7871949,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0628_S3_L004_R2_001.fastq.gz FS_WT0628_S3_L004_R1_001.fastq.gz FS_WT0628_S3_L004_I1_001.fastq.gz,fastq fastq fastq,3476431706.0,27373478.0,GSM7871949 r4,0:8 1:28 2:91,A:715940083;C:546111535;G:642639757;T:585816460;N:478663,8,28,91,,715940083,546111535,642639757,585816460,478663,SRX22289209,SRS19340293,SRA1742079,Boston University,Boston University,1,0.86857,,0.17561,,0.84094,,0.63847,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28711,SRR26588123,SRX22289208,SRS19340290,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 7.0 mm,GSM7871948,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871948,GSM7871948: WT 7.0 mm; Danio rerio; RNA Seq,GSM7871948 r1,GSM7871948,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0621_S1_L001_R2_001.fastq.gz FS_WT0621_S1_L001_R1_001.fastq.gz FS_WT0621_S1_L001_I1_001.fastq.gz,fastq fastq fastq,4296091865.0,33827495.0,GSM7871948 r1,0:8 1:28 2:91,A:873692918;C:671758488;G:778592608;T:753844494;N:413537,8,28,91,,873692918,671758488,778592608,753844494,413537,SRX22289208,SRS19340290,SRA1742079,Boston University,Boston University,1,0.88226,,0.23142,,0.80811,,0.58869,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28712,SRR26588124,SRX22289208,SRS19340290,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 7.0 mm,GSM7871948,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871948,GSM7871948: WT 7.0 mm; Danio rerio; RNA Seq,GSM7871948 r1,GSM7871948,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0621_S1_L002_R2_001.fastq.gz FS_WT0621_S1_L002_R1_001.fastq.gz FS_WT0621_S1_L002_I1_001.fastq.gz,fastq fastq fastq,4219879546.0,33227398.0,GSM7871948 r2,0:8 1:28 2:91,A:858665689;C:660231321;G:764062561;T:740359496;N:374151,8,28,91,,858665689,660231321,764062561,740359496,374151,SRX22289208,SRS19340290,SRA1742079,Boston University,Boston University,1,0.8833,,0.23028,,0.80734,,0.5998,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28713,SRR26588125,SRX22289208,SRS19340290,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 7.0 mm,GSM7871948,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871948,GSM7871948: WT 7.0 mm; Danio rerio; RNA Seq,GSM7871948 r1,GSM7871948,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0621_S1_L003_R2_001.fastq.gz FS_WT0621_S1_L003_R1_001.fastq.gz FS_WT0621_S1_L003_I1_001.fastq.gz,fastq fastq fastq,4341378795.0,34184085.0,GSM7871948 r3,0:8 1:28 2:91,A:882850653;C:681021491;G:786172206;T:760063970;N:643415,8,28,91,,882850653,681021491,786172206,760063970,643415,SRX22289208,SRS19340290,SRA1742079,Boston University,Boston University,1,0.88158,,0.23138,,0.80921,,0.5997,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28714,SRR26588126,SRX22289208,SRS19340290,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 7.0 mm,GSM7871948,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871948,GSM7871948: WT 7.0 mm; Danio rerio; RNA Seq,GSM7871948 r1,GSM7871948,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0621_S1_L004_R2_001.fastq.gz FS_WT0621_S1_L004_R1_001.fastq.gz FS_WT0621_S1_L004_I1_001.fastq.gz,fastq fastq fastq,4270514446.0,33626098.0,GSM7871948 r4,0:8 1:28 2:91,A:868634109;C:669284353;G:773305808;T:748175261;N:575387,8,28,91,,868634109,669284353,773305808,748175261,575387,SRX22289208,SRS19340290,SRA1742079,Boston University,Boston University,1,0.8822,,0.23032,,0.80695,,0.58745,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28715,SRR26588127,SRX22289207,SRS19340289,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 5.8 mm,GSM7871947,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871947,GSM7871947: sp7 mutant 5.8 mm; Danio rerio; RNA Seq,GSM7871947 r1,GSM7871947,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0628_S4_L001_R2_001.fastq.gz FS_Mutant0628_S4_L001_R1_001.fastq.gz FS_Mutant0628_S4_L001_I1_001.fastq.gz,fastq fastq fastq,3870633229.0,30477427.0,GSM7871947 r1,0:8 1:28 2:91,A:784323459;C:609892390;G:730737771;T:648119651;N:372586,8,28,91,,784323459,609892390,730737771,648119651,372586,SRX22289207,SRS19340289,SRA1742079,Boston University,Boston University,1,0.83967,,0.19678,,0.84027,,0.62798,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28716,SRR26588128,SRX22289207,SRS19340289,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 5.8 mm,GSM7871947,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871947,GSM7871947: sp7 mutant 5.8 mm; Danio rerio; RNA Seq,GSM7871947 r1,GSM7871947,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0628_S4_L002_R2_001.fastq.gz FS_Mutant0628_S4_L002_R1_001.fastq.gz FS_Mutant0628_S4_L002_I1_001.fastq.gz,fastq fastq fastq,3795705896.0,29887448.0,GSM7871947 r2,0:8 1:28 2:91,A:769584134;C:598310890;G:715720368;T:635803045;N:339331,8,28,91,,769584134,598310890,715720368,635803045,339331,SRX22289207,SRS19340289,SRA1742079,Boston University,Boston University,1,0.83992,,0.199,,0.84094,,0.63528,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28717,SRR26588129,SRX22289207,SRS19340289,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 5.8 mm,GSM7871947,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871947,GSM7871947: sp7 mutant 5.8 mm; Danio rerio; RNA Seq,GSM7871947 r1,GSM7871947,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0628_S4_L003_I1_001.fastq.gz FS_Mutant0628_S4_L003_R1_001.fastq.gz FS_Mutant0628_S4_L003_R2_001.fastq.gz,fastq fastq fastq,3882075802.0,30567526.0,GSM7871947 r3,0:8 1:28 2:91,A:786373431;C:613286785;G:731993747;T:649408434;N:582469,8,28,91,,786373431,613286785,731993747,649408434,582469,SRX22289207,SRS19340289,SRA1742079,Boston University,Boston University,1,0.83867,,0.19884,,0.83826,,0.63213,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28718,SRR26588130,SRX22289207,SRS19340289,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 5.8 mm,GSM7871947,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871947,GSM7871947: sp7 mutant 5.8 mm; Danio rerio; RNA Seq,GSM7871947 r1,GSM7871947,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0628_S4_L004_R2_001.fastq.gz FS_Mutant0628_S4_L004_R1_001.fastq.gz FS_Mutant0628_S4_L004_I1_001.fastq.gz,fastq fastq fastq,3821331575.0,30089225.0,GSM7871947 r4,0:8 1:28 2:91,A:774445827;C:603171063;G:720511073;T:639476444;N:515068,8,28,91,,774445827,603171063,720511073,639476444,515068,SRX22289207,SRS19340289,SRA1742079,Boston University,Boston University,1,0.84008,,0.19754,,0.84076,,0.63418,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28719,SRR26588131,SRX22289206,SRS19340291,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 7.0 mm,GSM7871946,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant  7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871946,GSM7871946: sp7 mutant  7.0 mm; Danio rerio; RNA Seq,GSM7871946 r1,GSM7871946,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0621_S2_L001_I1_001.fastq.gz FS_Mutant0621_S2_L001_R1_001.fastq.gz FS_Mutant0621_S2_L001_R2_001.fastq.gz,fastq fastq fastq,4256651761.0,33516943.0,GSM7871946 r1,0:8 1:28 2:91,A:862245132;C:673711733;G:766388204;T:747287820;N:408924,8,28,91,,862245132,673711733,766388204,747287820,408924,SRX22289206,SRS19340291,SRA1742079,Boston University,Boston University,1,0.89937,,0.20157,,0.80691,,0.60147,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28720,SRR26588132,SRX22289206,SRS19340291,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 7.0 mm,GSM7871946,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant  7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871946,GSM7871946: sp7 mutant  7.0 mm; Danio rerio; RNA Seq,GSM7871946 r1,GSM7871946,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0621_S2_L002_I1_001.fastq.gz FS_Mutant0621_S2_L002_R1_001.fastq.gz FS_Mutant0621_S2_L002_R2_001.fastq.gz,fastq fastq fastq,4173795437.0,32864531.0,GSM7871946 r2,0:8 1:28 2:91,A:846056609;C:660910650;G:750849639;T:732486246;N:369177,8,28,91,,846056609,660910650,750849639,732486246,369177,SRX22289206,SRS19340291,SRA1742079,Boston University,Boston University,1,0.89896,,0.20107,,0.80415,,0.60881,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28721,SRR26588133,SRX22289206,SRS19340291,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 7.0 mm,GSM7871946,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant  7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871946,GSM7871946: sp7 mutant  7.0 mm; Danio rerio; RNA Seq,GSM7871946 r1,GSM7871946,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0621_S2_L003_I1_001.fastq.gz FS_Mutant0621_S2_L003_R1_001.fastq.gz FS_Mutant0621_S2_L003_R2_001.fastq.gz,fastq fastq fastq,4291089081.0,33788103.0,GSM7871946 r3,0:8 1:28 2:91,A:869084749;C:681276277;G:772278057;T:751443489;N:634801,8,28,91,,869084749,681276277,772278057,751443489,634801,SRX22289206,SRS19340291,SRA1742079,Boston University,Boston University,1,0.89995,,0.20079,,0.80505,,0.60752,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28722,SRR26588134,SRX22289206,SRS19340291,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 7.0 mm,GSM7871946,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant  7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871946,GSM7871946: sp7 mutant  7.0 mm; Danio rerio; RNA Seq,GSM7871946 r1,GSM7871946,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0621_S2_L004_I1_001.fastq.gz FS_Mutant0621_S2_L004_R1_001.fastq.gz FS_Mutant0621_S2_L004_R2_001.fastq.gz,fastq fastq fastq,4221057598.0,33236674.0,GSM7871946 r4,0:8 1:28 2:91,A:855377679;C:669535108;G:759458317;T:739600774;N:565456,8,28,91,,855377679,669535108,759458317,739600774,565456,SRX22289206,SRS19340291,SRA1742079,Boston University,Boston University,1,0.90012,,0.20095,,0.80562,,0.60729,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
29197,SRR27321690,SRX22998813,SRS19963383,SRP479569,PRJNA1055522,Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin,GSE251828,Transcriptome Analysis,This study investigated the cell composition and lineage relationships of FACS fluorescence activated cell sorting enriched epidermal  bone forming osteoblast and non osteoblast blastemal fin regenerate cells by single cell sc RNA sequencing. The repetitive cell harvesting in four week intervals revealed a constant gene regulation over four successive regeneration rounds in the early outgrowth stage. In addition  the sc RNA dataset uncovered a potential lineage relationship between distal blastema cells and osteoblasts during fin regeneration. These findings  together with the identification of novel fin regenerate markers  advance our understanding of complex tissue regeneration in zebrafish. Overall design: To study potentially underrepresented cell populations during zebrafish fin regeneration  we harvested single cells and FACS enriched for siam+  shha+  osterix+  RUNX2+ cells via respective mCherry and GFP reporter fluorophores. We performed gene expression analysis using data obtained from RNA seq of enriched cells from 4 successive regeneration stages at 3 dpa.,,pubmed:38318374,,4th round of regeneration,GSM7988809,,source name:Fin|tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation|geo loc name:missing|collection date:missing,4th round of regeneration,A reference based on GRCz10  Ensembl annotation e98 was created  by first adding the sequences of gfp and mCherry as separate chromosomes to the fa file and the gtf file and then building the cellranger reference using cellranger mkref v3.0.0 fastq files were processed with `cellranger count` from 10X genomics version 3.0.0 Assembly: GRCz10 Supplementary files format and content: HDF5 Feature Barcode Matrix Format.,Fin,Fin regenerates of quadruple transgenic fish [Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259] were harvested at 3 dpa  cut into small pieces with a scalpel and transferred into 1 ml collagenase dispase solution 1 mg/ml in PBS  Roche #10269638001 for 10 min at 28°C. The sample was pipetted slowly up and down with an elongated  flame polished Pasteur pipette. The procedure was repeated 4 times with decreasing inner tip diameters of the Pasteur pipettes until a homogenous solution was obtained. The dissociates were poured onto an equilibrated 70 µm cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2  Gibco #12082739. post centrifugation 15 minutes  1800 rpm  4°C  the supernatant was discarded and the remaining cell pellet resuspended in 500 µl 2% BSA in PBS. Calcein violet 1µl 10mM  Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet  GFP and mCherry+ cells were collected in 50 µl 2% BSA in PBS via fluorescence activated cell sorting BD LSR Fortessa and processed for single cell RNA sequencing analysis based on 10X Genomics 10X Chromium system  10X library preparation according to the manufacturer's instructions.,For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell 3’ RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer’s guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.,,tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation,GSM7988809,GSM7988809: 4th round of regeneration; Danio rerio; RNA Seq,GSM7988809 r1,GSM7988809,1,For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell three prime RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer's guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP479569,,,L33268_osteoblasts_reg4_R2.fastq.gz L33268_osteoblasts_reg4_R1.fastq.gz,fastq fastq,7429523805.0,89512335.0,GSM7988809 r1,0:26 1:57,A:2056160949;C:1638835280;G:1683264344;T:2047119393;N:4143839,26,57,,,2056160949,1638835280,1683264344,2047119393,4143839,SRX22998813,SRS19963383,SRA1774238,"Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden","Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden",2,0.00833,0.93478,0.00199,0.12451,0.9849,0.82418,0.46227,0.53386,26,57,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-12-21,Undetermined,Undetermined,Fin,Surface Structure
29198,SRR27321691,SRX22998812,SRS19963382,SRP479569,PRJNA1055522,Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin,GSE251828,Transcriptome Analysis,This study investigated the cell composition and lineage relationships of FACS fluorescence activated cell sorting enriched epidermal  bone forming osteoblast and non osteoblast blastemal fin regenerate cells by single cell sc RNA sequencing. The repetitive cell harvesting in four week intervals revealed a constant gene regulation over four successive regeneration rounds in the early outgrowth stage. In addition  the sc RNA dataset uncovered a potential lineage relationship between distal blastema cells and osteoblasts during fin regeneration. These findings  together with the identification of novel fin regenerate markers  advance our understanding of complex tissue regeneration in zebrafish. Overall design: To study potentially underrepresented cell populations during zebrafish fin regeneration  we harvested single cells and FACS enriched for siam+  shha+  osterix+  RUNX2+ cells via respective mCherry and GFP reporter fluorophores. We performed gene expression analysis using data obtained from RNA seq of enriched cells from 4 successive regeneration stages at 3 dpa.,,pubmed:38318374,,3rd round of regeneration,GSM7988808,,source name:Fin|tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation|geo loc name:missing|collection date:missing,3rd round of regeneration,A reference based on GRCz10  Ensembl annotation e98 was created  by first adding the sequences of gfp and mCherry as separate chromosomes to the fa file and the gtf file and then building the cellranger reference using cellranger mkref v3.0.0 fastq files were processed with `cellranger count` from 10X genomics version 3.0.0 Assembly: GRCz10 Supplementary files format and content: HDF5 Feature Barcode Matrix Format.,Fin,Fin regenerates of quadruple transgenic fish [Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259] were harvested at 3 dpa  cut into small pieces with a scalpel and transferred into 1 ml collagenase dispase solution 1 mg/ml in PBS  Roche #10269638001 for 10 min at 28°C. The sample was pipetted slowly up and down with an elongated  flame polished Pasteur pipette. The procedure was repeated 4 times with decreasing inner tip diameters of the Pasteur pipettes until a homogenous solution was obtained. The dissociates were poured onto an equilibrated 70 µm cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2  Gibco #12082739. post centrifugation 15 minutes  1800 rpm  4°C  the supernatant was discarded and the remaining cell pellet resuspended in 500 µl 2% BSA in PBS. Calcein violet 1µl 10mM  Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet  GFP and mCherry+ cells were collected in 50 µl 2% BSA in PBS via fluorescence activated cell sorting BD LSR Fortessa and processed for single cell RNA sequencing analysis based on 10X Genomics 10X Chromium system  10X library preparation according to the manufacturer's instructions.,For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell 3’ RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer’s guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.,,tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation,GSM7988808,GSM7988808: 3rd round of regeneration; Danio rerio; RNA Seq,GSM7988808 r1,GSM7988808,1,For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell three prime RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer's guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP479569,,,L33267_osteoblasts_reg3_R1.fastq.gz L33267_osteoblasts_reg3_R2.fastq.gz,fastq fastq,5171923722.0,62312334.0,GSM7988808 r1,0:26 1:57,A:1429339406;C:1125953827;G:1205184308;T:1408611366;N:2834815,26,57,,,1429339406,1125953827,1205184308,1408611366,2834815,SRX22998812,SRS19963382,SRA1774238,"Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden","Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden",2,0.01041,0.92057,0.00236,0.13516,0.98198,0.82244,0.45267,0.53338,26,57,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-12-21,Undetermined,Undetermined,Fin,Surface Structure
29199,SRR27321692,SRX22998811,SRS19963381,SRP479569,PRJNA1055522,Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin,GSE251828,Transcriptome Analysis,This study investigated the cell composition and lineage relationships of FACS fluorescence activated cell sorting enriched epidermal  bone forming osteoblast and non osteoblast blastemal fin regenerate cells by single cell sc RNA sequencing. The repetitive cell harvesting in four week intervals revealed a constant gene regulation over four successive regeneration rounds in the early outgrowth stage. In addition  the sc RNA dataset uncovered a potential lineage relationship between distal blastema cells and osteoblasts during fin regeneration. These findings  together with the identification of novel fin regenerate markers  advance our understanding of complex tissue regeneration in zebrafish. Overall design: To study potentially underrepresented cell populations during zebrafish fin regeneration  we harvested single cells and FACS enriched for siam+  shha+  osterix+  RUNX2+ cells via respective mCherry and GFP reporter fluorophores. We performed gene expression analysis using data obtained from RNA seq of enriched cells from 4 successive regeneration stages at 3 dpa.,,pubmed:38318374,,2nd round of regeneration,GSM7988807,,source name:Fin|tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation|geo loc name:missing|collection date:missing,2nd round of regeneration,A reference based on GRCz10  Ensembl annotation e98 was created  by first adding the sequences of gfp and mCherry as separate chromosomes to the fa file and the gtf file and then building the cellranger reference using cellranger mkref v3.0.0 fastq files were processed with `cellranger count` from 10X genomics version 3.0.0 Assembly: GRCz10 Supplementary files format and content: HDF5 Feature Barcode Matrix Format.,Fin,Fin regenerates of quadruple transgenic fish [Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259] were harvested at 3 dpa  cut into small pieces with a scalpel and transferred into 1 ml collagenase dispase solution 1 mg/ml in PBS  Roche #10269638001 for 10 min at 28°C. The sample was pipetted slowly up and down with an elongated  flame polished Pasteur pipette. The procedure was repeated 4 times with decreasing inner tip diameters of the Pasteur pipettes until a homogenous solution was obtained. The dissociates were poured onto an equilibrated 70 µm cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2  Gibco #12082739. post centrifugation 15 minutes  1800 rpm  4°C  the supernatant was discarded and the remaining cell pellet resuspended in 500 µl 2% BSA in PBS. Calcein violet 1µl 10mM  Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet  GFP and mCherry+ cells were collected in 50 µl 2% BSA in PBS via fluorescence activated cell sorting BD LSR Fortessa and processed for single cell RNA sequencing analysis based on 10X Genomics 10X Chromium system  10X library preparation according to the manufacturer's instructions.,For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell 3’ RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer’s guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.,,tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation,GSM7988807,GSM7988807: 2nd round of regeneration; Danio rerio; RNA Seq,GSM7988807 r1,GSM7988807,1,For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell three prime RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer's guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP479569,,,L32508_osteoblasts_reg2_R1.fastq.gz L32508_osteoblasts_reg2_R2.fastq.gz,fastq fastq,6922720659.0,83406273.0,GSM7988807 r1,0:26 1:57,A:1901173243;C:1540845413;G:1598673449;T:1877295749;N:4732805,26,57,,,1901173243,1540845413,1598673449,1877295749,4732805,SRX22998811,SRS19963381,SRA1774238,"Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden","Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden",2,0.00257,0.93924,0.00083,0.10412,0.99474,0.83023,0.47435,0.51839,26,57,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-12-21,Undetermined,Undetermined,Fin,Surface Structure
29200,SRR27321693,SRX22998810,SRS19963380,SRP479569,PRJNA1055522,Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin,GSE251828,Transcriptome Analysis,This study investigated the cell composition and lineage relationships of FACS fluorescence activated cell sorting enriched epidermal  bone forming osteoblast and non osteoblast blastemal fin regenerate cells by single cell sc RNA sequencing. The repetitive cell harvesting in four week intervals revealed a constant gene regulation over four successive regeneration rounds in the early outgrowth stage. In addition  the sc RNA dataset uncovered a potential lineage relationship between distal blastema cells and osteoblasts during fin regeneration. These findings  together with the identification of novel fin regenerate markers  advance our understanding of complex tissue regeneration in zebrafish. Overall design: To study potentially underrepresented cell populations during zebrafish fin regeneration  we harvested single cells and FACS enriched for siam+  shha+  osterix+  RUNX2+ cells via respective mCherry and GFP reporter fluorophores. We performed gene expression analysis using data obtained from RNA seq of enriched cells from 4 successive regeneration stages at 3 dpa.,,pubmed:38318374,,1st round of regeneration,GSM7988806,,source name:Fin|tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation|geo loc name:missing|collection date:missing,1st round of regeneration,A reference based on GRCz10  Ensembl annotation e98 was created  by first adding the sequences of gfp and mCherry as separate chromosomes to the fa file and the gtf file and then building the cellranger reference using cellranger mkref v3.0.0 fastq files were processed with `cellranger count` from 10X genomics version 3.0.0 Assembly: GRCz10 Supplementary files format and content: HDF5 Feature Barcode Matrix Format.,Fin,Fin regenerates of quadruple transgenic fish [Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259] were harvested at 3 dpa  cut into small pieces with a scalpel and transferred into 1 ml collagenase dispase solution 1 mg/ml in PBS  Roche #10269638001 for 10 min at 28°C. The sample was pipetted slowly up and down with an elongated  flame polished Pasteur pipette. The procedure was repeated 4 times with decreasing inner tip diameters of the Pasteur pipettes until a homogenous solution was obtained. The dissociates were poured onto an equilibrated 70 µm cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2  Gibco #12082739. post centrifugation 15 minutes  1800 rpm  4°C  the supernatant was discarded and the remaining cell pellet resuspended in 500 µl 2% BSA in PBS. Calcein violet 1µl 10mM  Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet  GFP and mCherry+ cells were collected in 50 µl 2% BSA in PBS via fluorescence activated cell sorting BD LSR Fortessa and processed for single cell RNA sequencing analysis based on 10X Genomics 10X Chromium system  10X library preparation according to the manufacturer's instructions.,For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell 3’ RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer’s guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.,,tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation,GSM7988806,GSM7988806: 1st round of regeneration; Danio rerio; RNA Seq,GSM7988806 r1,GSM7988806,1,For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell three prime RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer's guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP479569,,,L32023_osteoblasts_reg1_R1.fastq.gz L32023_osteoblasts_reg1_R2.fastq.gz,fastq fastq,15070528207.0,181572629.0,GSM7988806 r1,0:26 1:57,A:4238593010;C:3314457079;G:3500292725;T:4013398538;N:3786855,26,57,,,4238593010,3314457079,3500292725,4013398538,3786855,SRX22998810,SRS19963380,SRA1774238,"Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden","Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden",2,0.01031,0.92947,0.00392,0.17331,0.98526,0.81815,0.4321,0.54688,26,57,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-12-21,Undetermined,Undetermined,Fin,Surface Structure
29201,SRR27319715,SRX22996941,SRS19961590,SRP479504,PRJNA1055557,Border zone cardiomyocytes and macrophages contribute to remodeling of the extracellular matrix to promote cardiomyocyte invasion during zebrafish cardiac regeneration,GSE251856,Other,Despite numerous advances in our understanding of zebrafish cardiac regeneration  an aspect that remains less studied is how newly proliferated cardiomyocytes invade  and eventually replace  the collagen containing fibrotic tissue following injury.  Here  we provide an in depth analysis of the process of cardiomyocyte invasion and migration using live imaging and histological approaches.  We observed a close interaction between protruding cardiomyocytes and macrophages at the wound border zone  and irf8 mutant zebrafish  which largely lack macrophages  exhibited defects in extracellular matrix ECM remodeling and cardiomyocyte protrusion into the injured area.  Using a resident macrophage ablation model  we show that defects in ECM remodeling at the border zone and subsequent cardiomyocyte protrusion can be partly attributed to a population of resident macrophages.  Single cell RNA sequencing analysis of cells at the wound border revealed a population of cardiomyocytes and macrophages with fibroblast like gene expression signatures  including the expression of genes encoding ECM structural proteins and ECM remodeling proteins.  The expression of mmp14b  which encodes a membrane anchored matrix metalloproteinase  was restricted to cells in the border zone and genetic deletion of mmp14b led to a decrease in 1 collagen degradation at the border zone  2 macrophage recruitment to the border zone  and 3 subsequent cardiomyocyte invasion.  Furthermore  cardiomyocyte specific overexpression of mmp14b was sufficient to enhance cardiomyocyte invasion both into the injured area and along the apical surface of the wound.  Altogether  our data shed important insights into the process of cardiomyocyte invasion of the collagen containing injured tissue during cardiac regeneration.  They further suggest that cardiomyocytes and resident macrophages contribute to ECM remodeling at the border zone to promote cardiomyocyte replenishment of the fibrotic injured tissue. Overall design: The border zone of regenerating wild type zebrafish hearts at 7 dpci was microdissected and subjected to scRNA seq,,pubmed:39962064;pubmed:40268967,,scRNA seq of wild type border z1 cells of regenerating hearts at 7 dpci,GSM7989198,,source name:Heart|tissue:Heart|genotype:Wild type|treatment:Hearts were cryoinjured and border z1 cells were microdissected at 7 dpci and pooled for scRNA seq|geo loc name:missing|collection date:missing,scRNA seq of wild type border z1 cells of regenerating hearts at 7 dpci,Reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo. Preprocessed counts were further analysed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 23 cells in total that did not express more than 300 genes or had a mitochondrial content greater than 40%. Furthermore  we filtered 9874 genes if they were detected in less than 30 cells <0.01%. Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA  retaining 50 principal components. Subsequent steps  like low dimensional UMAP embedding and cell clustering via community detection  were based on the initial PCA. Final data visualization was done by scanpy and cellxgene packages. Assembly: danRer11 Supplementary files format and content: starsolo outputs,Heart,Zebrafish hearts were cryoinjured and extracted at 7 dpci.,Border zone cells from 8 hearts were pooled and tissue dissociation was performed using the Pierce Primary Cardiomyocyte Isolation kit according to manufacturer's instructions.  Cells were resuspended in DMEM with 10% FBS and 1x glutamate. The cell suspensions were depleted for dead cells using LeviCell 1.0 device Levitas Bio counted with MOX Z cell counter and diluted according to manufacturer’s protocol to obtain 10.000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol.,,tissue:Heart|genotype:Wild type|treatment:Hearts were cryoinjured and border z1 cells were microdissected at 7 dpci and pooled for scRNA seq,GSM7989198,GSM7989198: scRNA seq of wild type border z1 cells of regenerating hearts at 7 dpci; Danio rerio; RNA Seq,GSM7989198 r1,GSM7989198,1,Border zone cells from 8 hearts were pooled and tissue dissociation was performed using the Pierce Primary Cardiomyocyte Isolation kit according to manufacturer's instructions.  Cells were resuspended in DMEM with 10% FBS and 1x glutamate. The cell suspensions were depleted for dead cells using LeviCell 1.0 device Levitas Bio counted with MOX Z cell counter and diluted according to manufacturer's protocol to obtain 10.000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP479504,,,Arica_10x_Zebrafish_Borderzone_Lib_R2.fastq.gz Arica_10x_Zebrafish_Borderzone_Lib_R1.fastq.gz,fastq fastq,35579193737.0,447572139.0,GSM7989198 r1,0:28 1:51.49,A:9662436792;C:7884457111;G:8055970010;T:9787114480;N:189215344,28,51,,,9662436792,7884457111,8055970010,9787114480,189215344,SRX22996941,SRS19961590,SRA1774131,MPI for heart and lung research,MPI for heart and lung research,2,0.00237,0.94011,0.00086,0.09945,0.99571,0.81907,0.32746,0.60892,28,51,T,B,sc-like readlen,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-12-21,Undetermined,Undetermined,Heart,Cardiovascular System
30626,SRR27907720,SRX23567476,SRS20412967,SRP488787,PRJNA1074408,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [scRNA seq],GSE255303,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood  but genetic factors have implicated in genome wide association studies  including CTLA 4  an essential negative regulator of T cell activation. However  establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study  we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 /  zebrafish line. These mutant zebrafish exhibit reduced weight  along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes  disturbing immune system homeostasis. Moreover  single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression  along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally  Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly  supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether  these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: intestine leukocyte WT and KO Ctla 4 deficiency  of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.,,pubmed:40392591,,KO  scRNAseq,GSM8068833,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO|geo loc name:missing|collection date:missing,KO  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 μg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO,GSM8068833,GSM8068833: KO  scRNAseq; Danio rerio; RNA Seq,GSM8068833 r1,GSM8068833,1,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 μg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP488787,,loader:fastq load.py,KO_S1_L001_R2_001.fastq.gz KO_S1_L001_R1_001.fastq.gz,fastq fastq,40958285011.0,344187269.0,GSM8068833 r1,0:28 1:91,A:11614416767;C:9247684357;G:9480911439;T:10614469263;N:803185,28,91,,,11614416767,9247684357,9480911439,10614469263,803185,SRX23567476,SRS20412967,SRA1799569,zhejiang university,zhejiang university,2,0.00982,0.9431,0.00356,0.10625,0.99277,0.8187,0.41297,0.63838,28,91,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30627,SRR27907721,SRX23567475,SRS20412966,SRP488787,PRJNA1074408,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [scRNA seq],GSE255303,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood  but genetic factors have implicated in genome wide association studies  including CTLA 4  an essential negative regulator of T cell activation. However  establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study  we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 /  zebrafish line. These mutant zebrafish exhibit reduced weight  along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes  disturbing immune system homeostasis. Moreover  single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression  along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally  Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly  supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether  these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: intestine leukocyte WT and KO Ctla 4 deficiency  of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.,,pubmed:40392591,,WT  scRNAseq,GSM8068832,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Wildtype|geo loc name:missing|collection date:missing,WT  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 μg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:intestine|cell type:leukocyte|genotype:Wildtype,GSM8068832,GSM8068832: WT  scRNAseq; Danio rerio; RNA Seq,GSM8068832 r1,GSM8068832,1,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 μg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP488787,,loader:fastq load.py,WT_S1_L001_R1_001.fastq.gz WT_S1_L001_R2_001.fastq.gz,fastq fastq,36724066995.0,308605605.0,GSM8068832 r1,0:28 1:91,A:10425178276;C:8399183780;G:8411777361;T:9487202777;N:724801,28,91,,,10425178276,8399183780,8411777361,9487202777,724801,SRX23567475,SRS20412966,SRA1799569,zhejiang university,zhejiang university,2,0.01141,0.94944,0.0039,0.1092,0.99324,0.841,0.43558,0.73314,28,91,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
34072,SRR31040127,SRX26425404,SRS22944868,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited UI L004,GSM8581895,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart|geo loc name:missing|collection date:missing,Cited UI L004,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart,GSM8581895,GSM8581895: Cited UI L004; Danio rerio; RNA Seq,GSM8581895 r1,GSM8581895,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L004 R1 001.fastq.gz   read2PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L004 R2 001.fastq.gz   read3PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L004 I1 001.fastq.gz   read4PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L004 I2 001.fastq.gz,pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L004_I1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L004_I2_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L004_R1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L004_R2_001.fastq.gz,fastq fastq fastq fastq,8751034986.0,63413297.0,GSM8581895 r1,0:28 1:90 2:10 3:10,A:1848966031;C:1012706988;G:1157260676;T:1688231038;N:31997,28,90,10,10,1848966031,1012706988,1157260676,1688231038,31997,SRX26425404,SRS22944868,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34073,SRR31040128,SRX26425403,SRS22944867,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited UI L003,GSM8581894,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart|geo loc name:missing|collection date:missing,Cited UI L003,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart,GSM8581894,GSM8581894: Cited UI L003; Danio rerio; RNA Seq,GSM8581894 r1,GSM8581894,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L003 R1 001.fastq.gz   read2PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L003 R2 001.fastq.gz   read3PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L003 I1 001.fastq.gz   read4PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L003 I2 001.fastq.gz,pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L003_I1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L003_I2_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L003_R1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L003_R2_001.fastq.gz,fastq fastq fastq fastq,8965044420.0,64964090.0,GSM8581894 r1,0:28 1:90 2:10 3:10,A:1889187704;C:1042838950;G:1192357586;T:1722353910;N:29950,28,90,10,10,1889187704,1042838950,1192357586,1722353910,29950,SRX26425403,SRS22944867,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34074,SRR31040129,SRX26425402,SRS22944866,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited UI L002,GSM8581893,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart|geo loc name:missing|collection date:missing,Cited UI L002,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart,GSM8581893,GSM8581893: Cited UI L002; Danio rerio; RNA Seq,GSM8581893 r1,GSM8581893,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L002 R1 001.fastq.gz   read2PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L002 R2 001.fastq.gz   read3PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L002 I1 001.fastq.gz   read4PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L002 I2 001.fastq.gz,pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L002_I1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L002_I2_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L002_R1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L002_R2_001.fastq.gz,fastq fastq fastq fastq,9234521850.0,66916825.0,GSM8581893 r1,0:28 1:90 2:10 3:10,A:1942032508;C:1074923961;G:1229240783;T:1776284178;N:32820,28,90,10,10,1942032508,1074923961,1229240783,1776284178,32820,SRX26425402,SRS22944866,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34075,SRR31040130,SRX26425401,SRS22944865,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited UI L001,GSM8581892,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart|geo loc name:missing|collection date:missing,Cited UI L001,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart,GSM8581892,GSM8581892: Cited UI L001; Danio rerio; RNA Seq,GSM8581892 r1,GSM8581892,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L001 R1 001.fastq.gz   read2PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L001 R2 001.fastq.gz   read3PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L001 I1 001.fastq.gz   read4PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L001 I2 001.fastq.gz,pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L001_I1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L001_I2_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L001_R1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L001_R2_001.fastq.gz,fastq fastq fastq fastq,9307917288.0,67448676.0,GSM8581892 r1,0:28 1:90 2:10 3:10,A:1956920944;C:1083084138;G:1238610324;T:1791739835;N:25599,28,90,10,10,1956920944,1083084138,1238610324,1791739835,25599,SRX26425401,SRS22944865,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34076,SRR31040131,SRX26425400,SRS22944864,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited 3dpa L004,GSM8581891,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,Cited 3dpa L004,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation,GSM8581891,GSM8581891: Cited 3dpa L004; Danio rerio; RNA Seq,GSM8581891 r1,GSM8581891,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L004 R1 001.fastq.gz   read2PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L004 R2 001.fastq.gz   read3PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L004 I1 001.fastq.gz   read4PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L004 I2 001.fastq.gz,pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L004_I1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L004_I2_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L004_R1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L004_R2_001.fastq.gz,fastq fastq fastq fastq,7170951684.0,51963418.0,GSM8581891 r1,0:28 1:90 2:10 3:10,A:1540735099;C:805699399;G:919379467;T:1410866922;N:26733,28,90,10,10,1540735099,805699399,919379467,1410866922,26733,SRX26425400,SRS22944864,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34077,SRR31040132,SRX26425399,SRS22944863,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited 3dpa L003,GSM8581890,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,Cited 3dpa L003,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation,GSM8581890,GSM8581890: Cited 3dpa L003; Danio rerio; RNA Seq,GSM8581890 r1,GSM8581890,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L003 R1 001.fastq.gz   read2PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L003 R2 001.fastq.gz   read3PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L003 I1 001.fastq.gz   read4PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L003 I2 001.fastq.gz,pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L003_I1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L003_I2_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L003_R1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L003_R2_001.fastq.gz,fastq fastq fastq fastq,7291420716.0,52836382.0,GSM8581890 r1,0:28 1:90 2:10 3:10,A:1561481957;C:822744414;G:938546253;T:1432477210;N:24546,28,90,10,10,1561481957,822744414,938546253,1432477210,24546,SRX26425399,SRS22944863,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34078,SRR31040133,SRX26425398,SRS22944862,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited 3dpa L002,GSM8581889,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,Cited 3dpa L002,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation,GSM8581889,GSM8581889: Cited 3dpa L002; Danio rerio; RNA Seq,GSM8581889 r1,GSM8581889,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L002 R1 001.fastq.gz   read2PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L002 R2 001.fastq.gz   read3PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L002 I1 001.fastq.gz   read4PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L002 I2 001.fastq.gz,pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L002_I1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L002_I2_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L002_R1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L002_R2_001.fastq.gz,fastq fastq fastq fastq,7477578162.0,54185349.0,GSM8581889 r1,0:28 1:90 2:10 3:10,A:1599788142;C:843874544;G:963283854;T:1469708656;N:26214,28,90,10,10,1599788142,843874544,963283854,1469708656,26214,SRX26425398,SRS22944862,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34079,SRR31040134,SRX26425397,SRS22944861,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited 3dpa L001,GSM8581888,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,Cited 3dpa L001,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation,GSM8581888,GSM8581888: Cited 3dpa L001; Danio rerio; RNA Seq,GSM8581888 r1,GSM8581888,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L001 R1 001.fastq.gz   read2PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L001 R2 001.fastq.gz   read3PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L001 I1 001.fastq.gz   read4PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L001 I2 001.fastq.gz,pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L001_I1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L001_I2_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L001_R1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L001_R2_001.fastq.gz,fastq fastq fastq fastq,7511701146.0,54432617.0,GSM8581888 r1,0:28 1:90 2:10 3:10,A:1606850913;C:847555151;G:967521409;T:1476987489;N:20568,28,90,10,10,1606850913,847555151,967521409,1476987489,20568,SRX26425397,SRS22944861,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34080,SRR31040135,SRX26425396,SRS22944860,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT UI L004,GSM8581887,,source name:heart|tissue:heart|genotype:WT|treatment:Uninjured heart|geo loc name:missing|collection date:missing,WT UI L004,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:Uninjured heart,GSM8581887,GSM8581887: WT UI L004; Danio rerio; RNA Seq,GSM8581887 r1,GSM8581887,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L004 R1 001.fastq.gz   read2PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L004 R2 001.fastq.gz   read3PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L004 I1 001.fastq.gz   read4PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L004 I2 001.fastq.gz,WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L004_I1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L004_I2_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L004_R1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L004_R2_001.fastq.gz,fastq fastq fastq fastq,8744622816.0,63366832.0,GSM8581887 r1,0:28 1:90 2:10 3:10,A:1804235390;C:1112990195;G:1270205014;T:1515005620;N:578661,28,90,10,10,1804235390,1112990195,1270205014,1515005620,578661,SRX26425396,SRS22944860,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34081,SRR31040136,SRX26425395,SRS22944859,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT UI L003,GSM8581886,,source name:heart|tissue:heart|genotype:WT|treatment:Uninjured heart|geo loc name:missing|collection date:missing,WT UI L003,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:Uninjured heart,GSM8581886,GSM8581886: WT UI L003; Danio rerio; RNA Seq,GSM8581886 r1,GSM8581886,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L003 R1 001.fastq.gz   read2PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L003 R2 001.fastq.gz   read3PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L003 I1 001.fastq.gz   read4PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L003 I2 001.fastq.gz,WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L003_I1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L003_I2_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L003_R1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L003_R2_001.fastq.gz,fastq fastq fastq fastq,8629549722.0,62532969.0,GSM8581886 r1,0:28 1:90 2:10 3:10,A:1780671193;C:1097605584;G:1253098096;T:1495999781;N:592556,28,90,10,10,1780671193,1097605584,1253098096,1495999781,592556,SRX26425395,SRS22944859,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34082,SRR31040137,SRX26425394,SRS22944858,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT UI L002,GSM8581885,,source name:heart|tissue:heart|genotype:WT|treatment:Uninjured heart|geo loc name:missing|collection date:missing,WT UI L002,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:Uninjured heart,GSM8581885,GSM8581885: WT UI L002; Danio rerio; RNA Seq,GSM8581885 r1,GSM8581885,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L002 R1 001.fastq.gz   read2PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L002 R2 001.fastq.gz   read3PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L002 I1 001.fastq.gz   read4PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L002 I2 001.fastq.gz,WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L002_I1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L002_I2_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L002_R1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L002_R2_001.fastq.gz,fastq fastq fastq fastq,8810036748.0,63840846.0,GSM8581885 r1,0:28 1:90 2:10 3:10,A:1816298911;C:1122594552;G:1280394245;T:1525799551;N:588881,28,90,10,10,1816298911,1122594552,1280394245,1525799551,588881,SRX26425394,SRS22944858,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34083,SRR31040138,SRX26425393,SRS22944857,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT UI L001,GSM8581884,,source name:heart|tissue:heart|genotype:WT|treatment:Uninjured heart|geo loc name:missing|collection date:missing,WT UI L001,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:Uninjured heart,GSM8581884,GSM8581884: WT UI L001; Danio rerio; RNA Seq,GSM8581884 r1,GSM8581884,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L001 R1 001.fastq.gz   read2PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L001 R2 001.fastq.gz   read3PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L001 I1 001.fastq.gz   read4PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L001 I2 001.fastq.gz,WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L001_I1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L001_I2_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L001_R1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L001_R2_001.fastq.gz,fastq fastq fastq fastq,8890601838.0,64424651.0,GSM8581884 r1,0:28 1:90 2:10 3:10,A:1831803855;C:1133337909;G:1293064278;T:1539489836;N:522712,28,90,10,10,1831803855,1133337909,1293064278,1539489836,522712,SRX26425393,SRS22944857,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34084,SRR31040139,SRX26425392,SRS22944856,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT 3dpa L004,GSM8581883,,source name:heart|tissue:heart|genotype:WT|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,WT 3dpa L004,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:3 dy post amputation,GSM8581883,GSM8581883: WT 3dpa L004; Danio rerio; RNA Seq,GSM8581883 r1,GSM8581883,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L004 R1 001.fastq.gz   read2PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L004 R2 001.fastq.gz   read3PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L004 I1 001.fastq.gz   read4PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L004 I2 001.fastq.gz,WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L004_I1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L004_I2_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L004_R1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L004_R2_001.fastq.gz,fastq fastq fastq fastq,10259680380.0,74345510.0,GSM8581883 r1,0:28 1:90 2:10 3:10,A:2030501498;C:1372342288;G:1610608028;T:1676971327;N:672759,28,90,10,10,2030501498,1372342288,1610608028,1676971327,672759,SRX26425392,SRS22944856,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34085,SRR31040140,SRX26425391,SRS22944855,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT 3dpa L003,GSM8581882,,source name:heart|tissue:heart|genotype:WT|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,WT 3dpa L003,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:3 dy post amputation,GSM8581882,GSM8581882: WT 3dpa L003; Danio rerio; RNA Seq,GSM8581882 r1,GSM8581882,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L003 R1 001.fastq.gz   read2PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L003 R2 001.fastq.gz   read3PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L003 I1 001.fastq.gz   read4PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L003 I2 001.fastq.gz,WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L003_I1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L003_I2_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L003_R1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L003_R2_001.fastq.gz,fastq fastq fastq fastq,10153022940.0,73572630.0,GSM8581882 r1,0:28 1:90 2:10 3:10,A:2010560616;C:1356907781;G:1592695197;T:1660694697;N:678409,28,90,10,10,2010560616,1356907781,1592695197,1660694697,678409,SRX26425391,SRS22944855,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34086,SRR31040141,SRX26425390,SRS22944854,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT 3dpa L002,GSM8581881,,source name:heart|tissue:heart|genotype:WT|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,WT 3dpa L002,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:3 dy post amputation,GSM8581881,GSM8581881: WT 3dpa L002; Danio rerio; RNA Seq,GSM8581881 r1,GSM8581881,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L002 R1 001.fastq.gz   read2PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L002 R2 001.fastq.gz   read3PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L002 I1 001.fastq.gz   read4PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L002 I2 001.fastq.gz,WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L002_I1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L002_I2_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L002_R1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L002_R2_001.fastq.gz,fastq fastq fastq fastq,10374062784.0,75174368.0,GSM8581881 r1,0:28 1:90 2:10 3:10,A:2050663376;C:1389631407;G:1629809936;T:1694915558;N:672843,28,90,10,10,2050663376,1389631407,1629809936,1694915558,672843,SRX26425390,SRS22944854,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34087,SRR31040142,SRX26425389,SRS22944853,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT 3dpa L001,GSM8581880,,source name:heart|tissue:heart|genotype:WT|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,WT 3dpa L001,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:3 dy post amputation,GSM8581880,GSM8581880: WT 3dpa L001; Danio rerio; RNA Seq,GSM8581880 r1,GSM8581880,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L001 R1 001.fastq.gz   read2PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L001 R2 001.fastq.gz   read3PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L001 I1 001.fastq.gz   read4PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L001 I2 001.fastq.gz,WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L001_I1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L001_I2_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L001_R1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L001_R2_001.fastq.gz,fastq fastq fastq fastq,10577377770.0,76647665.0,GSM8581880 r1,0:28 1:90 2:10 3:10,A:2089361892;C:1417156705;G:1662751139;T:1728402830;N:617284,28,90,10,10,2089361892,1417156705,1662751139,1728402830,617284,SRX26425389,SRS22944853,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
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,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
35816,SRR33052294,SRX28317427,SRS24656196,SRP577565,PRJNA1248471,P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3ß Inhibitors with Anti Neurodegenerative Efficacy,GSE294097,Transcriptome Analysis,Spatial transcriptome sequencing technology has provided high resolution transcriptome data for studying the molecular mechanism of Tau P301S mediating Alzheimer's disease like pathological changes in zebrafish  providing a unique insight into the pathogenesis of tau pathology mediated cell cell interactions in AD. Overall design: This study utilized four Danio rerio lines: wild type WT and three transgenic lines AD3  AD4  AD5 expressing human Tau protein with the P301S mutation Tau P301S. All transgenic lines were generated via stable integration of the human TAU P301S transgene.,,,,WT,GSM8898657,,source name:Brain|tissue:Brain|geo loc name:missing|collection date:missing,WT,Reads were processed using the SAW 7.1.0 pipeline with default and recommended parameters. Assembly: GRCz11 Supplementary files format and content: Mask files  matrix files and image files.,Brain,,Tissue sections were adhered to the Stereo seq chip generated by BGI  China surface and incubated at 37℃ for 3 minutes. Then  the sections were fixed in methanol and incubated for 40 minutes at  20℃ before Stereo seq library preparation. Where indicated  the same sections were stained with nucleic acid dye Thermo fisher  Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L  tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma  P7000 in 0.01 M HCl buffer  incubated at 37℃ for 5 minutes and then washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42℃ using SuperScript II Invitrogen  18064 014  10 U/ml reverse transcriptase  1 mM dNTPs  1 M betaine solution PCR reagent  7.5 mM MgCl2  5 mM DTT  2 U/ml RNase inhibitor  2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription  tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl  25 mM EDTA  100 mM NaCl  0.5% SDS at 55℃ for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme  cDNA Release buffer treatment for over night at 55℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo  Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55℃ for 10 minutes  post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product  1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer  0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95℃ 5 minutes  13 cycles of 98℃ 20 seconds  58℃ 20 seconds and 72℃ 30 seconds  and 1 cycle of 72℃ 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153  used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.,,tissue:Brain,GSM8898657,GSM8898657: WT; Danio rerio; RNA Seq,GSM8898657 r1,GSM8898657,1,Tissue sections were adhered to the Stereo seq chip generated by BGI  China surface and incubated at 37℃ for 3 minutes. Then  the sections were fixed in methanol and incubated for 40 minutes at  20℃ before Stereo seq library preparation. Where indicated  the same sections were stained with nucleic acid dye Thermo fisher  Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L  tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma  P7000 in 0.01 M HCl buffer  incubated at 37℃ for 5 minutes and then washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42℃ using SuperScript II Invitrogen  18064 014  10 U/ml reverse transcriptase  1 mM dNTPs  1 M betaine solution PCR reagent  7.5 mM MgCl2  5 mM DTT  2 U/ml RNase inhibitor  2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription  tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl  25 mM EDTA  100 mM NaCl  0.5% SDS at 55℃ for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme  cDNA Release buffer treatment for over night at 55℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo  Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55℃ for 10 minutes  post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product  1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer  0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95℃ 5 minutes  13 cycles of 98℃ 20 seconds  58℃ 20 seconds and 72℃ 30 seconds  and 1 cycle of 72℃ 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153  used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP577565,,,WT_L01_read_1.fq.gz WT_L01_read_2.fq.gz,fastq fastq,74425524705.0,551300183.0,GSM8898657 r1,0:35 1:100,A:19898122181;C:17423066656;G:16942100032;T:20160847006;N:1388830,35,100,,,19898122181,17423066656,16942100032,20160847006,1388830,SRX28317427,SRS24656196,SRA2109204,ShanTou University,ShanTou University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,bgi,bgi,unknown,cdna_unspecified,unknown,sc,unknown,unknown,,China,2025-04-09,Undetermined,Undetermined,Brain,Nervous System
35817,SRR33052295,SRX28317426,SRS24656195,SRP577565,PRJNA1248471,P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3ß Inhibitors with Anti Neurodegenerative Efficacy,GSE294097,Transcriptome Analysis,Spatial transcriptome sequencing technology has provided high resolution transcriptome data for studying the molecular mechanism of Tau P301S mediating Alzheimer's disease like pathological changes in zebrafish  providing a unique insight into the pathogenesis of tau pathology mediated cell cell interactions in AD. Overall design: This study utilized four Danio rerio lines: wild type WT and three transgenic lines AD3  AD4  AD5 expressing human Tau protein with the P301S mutation Tau P301S. All transgenic lines were generated via stable integration of the human TAU P301S transgene.,,,,AD5,GSM8898656,,source name:Brain|tissue:Brain|geo loc name:missing|collection date:missing,AD5,Reads were processed using the SAW 7.1.0 pipeline with default and recommended parameters. Assembly: GRCz11 Supplementary files format and content: Mask files  matrix files and image files.,Brain,,Tissue sections were adhered to the Stereo seq chip generated by BGI  China surface and incubated at 37℃ for 3 minutes. Then  the sections were fixed in methanol and incubated for 40 minutes at  20℃ before Stereo seq library preparation. Where indicated  the same sections were stained with nucleic acid dye Thermo fisher  Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L  tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma  P7000 in 0.01 M HCl buffer  incubated at 37℃ for 5 minutes and then washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42℃ using SuperScript II Invitrogen  18064 014  10 U/ml reverse transcriptase  1 mM dNTPs  1 M betaine solution PCR reagent  7.5 mM MgCl2  5 mM DTT  2 U/ml RNase inhibitor  2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription  tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl  25 mM EDTA  100 mM NaCl  0.5% SDS at 55℃ for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme  cDNA Release buffer treatment for over night at 55℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo  Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55℃ for 10 minutes  post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product  1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer  0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95℃ 5 minutes  13 cycles of 98℃ 20 seconds  58℃ 20 seconds and 72℃ 30 seconds  and 1 cycle of 72℃ 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153  used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.,,tissue:Brain,GSM8898656,GSM8898656: AD5; Danio rerio; RNA Seq,GSM8898656 r1,GSM8898656,1,Tissue sections were adhered to the Stereo seq chip generated by BGI  China surface and incubated at 37℃ for 3 minutes. Then  the sections were fixed in methanol and incubated for 40 minutes at  20℃ before Stereo seq library preparation. Where indicated  the same sections were stained with nucleic acid dye Thermo fisher  Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L  tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma  P7000 in 0.01 M HCl buffer  incubated at 37℃ for 5 minutes and then washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42℃ using SuperScript II Invitrogen  18064 014  10 U/ml reverse transcriptase  1 mM dNTPs  1 M betaine solution PCR reagent  7.5 mM MgCl2  5 mM DTT  2 U/ml RNase inhibitor  2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription  tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl  25 mM EDTA  100 mM NaCl  0.5% SDS at 55℃ for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme  cDNA Release buffer treatment for over night at 55℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo  Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55℃ for 10 minutes  post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product  1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer  0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95℃ 5 minutes  13 cycles of 98℃ 20 seconds  58℃ 20 seconds and 72℃ 30 seconds  and 1 cycle of 72℃ 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153  used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP577565,,,AD5_L01_read_1.fq.gz AD5_L01_read_2.fq.gz,fastq fastq,84955633785.0,629300991.0,GSM8898656 r1,0:35 1:100,A:22736382740;C:20123949961;G:19583698932;T:22509389862;N:2212290,35,100,,,22736382740,20123949961,19583698932,22509389862,2212290,SRX28317426,SRS24656195,SRA2109204,ShanTou University,ShanTou University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,bgi,bgi,unknown,cdna_unspecified,unknown,sc,unknown,unknown,,China,2025-04-09,Undetermined,Undetermined,Brain,Nervous System
35818,SRR33052296,SRX28317425,SRS24656194,SRP577565,PRJNA1248471,P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3ß Inhibitors with Anti Neurodegenerative Efficacy,GSE294097,Transcriptome Analysis,Spatial transcriptome sequencing technology has provided high resolution transcriptome data for studying the molecular mechanism of Tau P301S mediating Alzheimer's disease like pathological changes in zebrafish  providing a unique insight into the pathogenesis of tau pathology mediated cell cell interactions in AD. Overall design: This study utilized four Danio rerio lines: wild type WT and three transgenic lines AD3  AD4  AD5 expressing human Tau protein with the P301S mutation Tau P301S. All transgenic lines were generated via stable integration of the human TAU P301S transgene.,,,,AD4,GSM8898655,,source name:Brain|tissue:Brain|geo loc name:missing|collection date:missing,AD4,Reads were processed using the SAW 7.1.0 pipeline with default and recommended parameters. Assembly: GRCz11 Supplementary files format and content: Mask files  matrix files and image files.,Brain,,Tissue sections were adhered to the Stereo seq chip generated by BGI  China surface and incubated at 37℃ for 3 minutes. Then  the sections were fixed in methanol and incubated for 40 minutes at  20℃ before Stereo seq library preparation. Where indicated  the same sections were stained with nucleic acid dye Thermo fisher  Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L  tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma  P7000 in 0.01 M HCl buffer  incubated at 37℃ for 5 minutes and then washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42℃ using SuperScript II Invitrogen  18064 014  10 U/ml reverse transcriptase  1 mM dNTPs  1 M betaine solution PCR reagent  7.5 mM MgCl2  5 mM DTT  2 U/ml RNase inhibitor  2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription  tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl  25 mM EDTA  100 mM NaCl  0.5% SDS at 55℃ for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme  cDNA Release buffer treatment for over night at 55℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo  Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55℃ for 10 minutes  post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product  1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer  0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95℃ 5 minutes  13 cycles of 98℃ 20 seconds  58℃ 20 seconds and 72℃ 30 seconds  and 1 cycle of 72℃ 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153  used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.,,tissue:Brain,GSM8898655,GSM8898655: AD4; Danio rerio; RNA Seq,GSM8898655 r1,GSM8898655,1,Tissue sections were adhered to the Stereo seq chip generated by BGI  China surface and incubated at 37℃ for 3 minutes. Then  the sections were fixed in methanol and incubated for 40 minutes at  20℃ before Stereo seq library preparation. Where indicated  the same sections were stained with nucleic acid dye Thermo fisher  Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L  tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma  P7000 in 0.01 M HCl buffer  incubated at 37℃ for 5 minutes and then washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42℃ using SuperScript II Invitrogen  18064 014  10 U/ml reverse transcriptase  1 mM dNTPs  1 M betaine solution PCR reagent  7.5 mM MgCl2  5 mM DTT  2 U/ml RNase inhibitor  2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription  tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl  25 mM EDTA  100 mM NaCl  0.5% SDS at 55℃ for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme  cDNA Release buffer treatment for over night at 55℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo  Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55℃ for 10 minutes  post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product  1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer  0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95℃ 5 minutes  13 cycles of 98℃ 20 seconds  58℃ 20 seconds and 72℃ 30 seconds  and 1 cycle of 72℃ 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153  used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP577565,,,AD4_L01_read_1.fq.gz AD4_L01_read_2.fq.gz,fastq fastq,44786077200.0,331748720.0,GSM8898655 r1,0:35 1:100,A:11725098079;C:10594300338;G:10327407801;T:12138018161;N:1252821,35,100,,,11725098079,10594300338,10327407801,12138018161,1252821,SRX28317425,SRS24656194,SRA2109204,ShanTou University,ShanTou University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,bgi,bgi,unknown,cdna_unspecified,unknown,sc,unknown,unknown,,China,2025-04-09,Undetermined,Undetermined,Brain,Nervous System
35819,SRR33052297,SRX28317424,SRS24656193,SRP577565,PRJNA1248471,P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3ß Inhibitors with Anti Neurodegenerative Efficacy,GSE294097,Transcriptome Analysis,Spatial transcriptome sequencing technology has provided high resolution transcriptome data for studying the molecular mechanism of Tau P301S mediating Alzheimer's disease like pathological changes in zebrafish  providing a unique insight into the pathogenesis of tau pathology mediated cell cell interactions in AD. Overall design: This study utilized four Danio rerio lines: wild type WT and three transgenic lines AD3  AD4  AD5 expressing human Tau protein with the P301S mutation Tau P301S. All transgenic lines were generated via stable integration of the human TAU P301S transgene.,,,,AD3,GSM8898654,,source name:Brain|tissue:Brain|geo loc name:missing|collection date:missing,AD3,Reads were processed using the SAW 7.1.0 pipeline with default and recommended parameters. Assembly: GRCz11 Supplementary files format and content: Mask files  matrix files and image files.,Brain,,Tissue sections were adhered to the Stereo seq chip generated by BGI  China surface and incubated at 37℃ for 3 minutes. Then  the sections were fixed in methanol and incubated for 40 minutes at  20℃ before Stereo seq library preparation. Where indicated  the same sections were stained with nucleic acid dye Thermo fisher  Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L  tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma  P7000 in 0.01 M HCl buffer  incubated at 37℃ for 5 minutes and then washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42℃ using SuperScript II Invitrogen  18064 014  10 U/ml reverse transcriptase  1 mM dNTPs  1 M betaine solution PCR reagent  7.5 mM MgCl2  5 mM DTT  2 U/ml RNase inhibitor  2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription  tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl  25 mM EDTA  100 mM NaCl  0.5% SDS at 55℃ for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme  cDNA Release buffer treatment for over night at 55℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo  Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55℃ for 10 minutes  post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product  1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer  0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95℃ 5 minutes  13 cycles of 98℃ 20 seconds  58℃ 20 seconds and 72℃ 30 seconds  and 1 cycle of 72℃ 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153  used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.,,tissue:Brain,GSM8898654,GSM8898654: AD3; Danio rerio; RNA Seq,GSM8898654 r1,GSM8898654,1,Tissue sections were adhered to the Stereo seq chip generated by BGI  China surface and incubated at 37℃ for 3 minutes. Then  the sections were fixed in methanol and incubated for 40 minutes at  20℃ before Stereo seq library preparation. Where indicated  the same sections were stained with nucleic acid dye Thermo fisher  Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L  tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma  P7000 in 0.01 M HCl buffer  incubated at 37℃ for 5 minutes and then washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42℃ using SuperScript II Invitrogen  18064 014  10 U/ml reverse transcriptase  1 mM dNTPs  1 M betaine solution PCR reagent  7.5 mM MgCl2  5 mM DTT  2 U/ml RNase inhibitor  2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription  tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl  25 mM EDTA  100 mM NaCl  0.5% SDS at 55℃ for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme  cDNA Release buffer treatment for over night at 55℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo  Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55℃ for 10 minutes  post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product  1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer  0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95℃ 5 minutes  13 cycles of 98℃ 20 seconds  58℃ 20 seconds and 72℃ 30 seconds  and 1 cycle of 72℃ 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153  used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP577565,,,AD3_L01_read_1.fq.gz AD3_L01_read_2.fq.gz,fastq fastq,60591288060.0,448824356.0,GSM8898654 r1,0:35 1:100,A:15920282345;C:14771409856;G:14276809765;T:15621229410;N:1556684,35,100,,,15920282345,14771409856,14276809765,15621229410,1556684,SRX28317424,SRS24656193,SRA2109204,ShanTou University,ShanTou University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,bgi,bgi,unknown,cdna_unspecified,unknown,sc,unknown,unknown,,China,2025-04-09,Undetermined,Undetermined,Brain,Nervous System
69558,SRR18901602,SRX14979859,SRS12729750,SRP371883,PRJNA831276,Lipid droplets are a metabolic vulnerability in melanoma,GSE201378,Transcriptome Analysis,Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma,,pubmed:37268606,,TEAZ scRNAseq,GSM6062264,,source name:Skin|tissue:Skin|cell type:melanoma,TEAZ scRNAseq,Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11,Skin,,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,tissue:Skin|cell type:melanoma,GSM6062264,GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq,GSM6062264 r1,GSM6062264,1,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,loader:fastq load.py,2544_PTEN_combined_IGO_11963_4_S2_L001_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L001_R2_001.fastq.gz,fastq fastq,9314576760.0,77621473.0,GSM6062264 r1,0:29 1:91,A:2571624849;C:2103171866;G:2248508025;T:2390911966;N:360054,29,91,,,2571624849,2103171866,2248508025,2390911966,360054,SRX14979859,SRS12729750,SRA1408865,"Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center","Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.00434,0.8777,0.00177,0.14429,0.99253,0.78492,0.35282,0.53036,29,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-04-23,Undetermined,Undetermined,Skin,Surface Structure
69559,SRR18901603,SRX14979859,SRS12729750,SRP371883,PRJNA831276,Lipid droplets are a metabolic vulnerability in melanoma,GSE201378,Transcriptome Analysis,Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma,,pubmed:37268606,,TEAZ scRNAseq,GSM6062264,,source name:Skin|tissue:Skin|cell type:melanoma,TEAZ scRNAseq,Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11,Skin,,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,tissue:Skin|cell type:melanoma,GSM6062264,GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq,GSM6062264 r1,GSM6062264,1,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,loader:fastq load.py,2544_PTEN_combined_IGO_11963_4_S2_L002_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L002_R2_001.fastq.gz,fastq fastq,9122357880.0,76019649.0,GSM6062264 r2,0:29 1:91,A:2521047948;C:2056950129;G:2200048731;T:2343919901;N:391171,29,91,,,2521047948,2056950129,2200048731,2343919901,391171,SRX14979859,SRS12729750,SRA1408865,"Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center","Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.00471,0.87992,0.00196,0.14374,0.99255,0.78476,0.35593,0.54484,29,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-04-23,Undetermined,Undetermined,Skin,Surface Structure
69560,SRR18901604,SRX14979859,SRS12729750,SRP371883,PRJNA831276,Lipid droplets are a metabolic vulnerability in melanoma,GSE201378,Transcriptome Analysis,Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma,,pubmed:37268606,,TEAZ scRNAseq,GSM6062264,,source name:Skin|tissue:Skin|cell type:melanoma,TEAZ scRNAseq,Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11,Skin,,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,tissue:Skin|cell type:melanoma,GSM6062264,GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq,GSM6062264 r1,GSM6062264,1,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,loader:fastq load.py,2544_PTEN_combined_IGO_11963_4_S2_L003_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L003_R2_001.fastq.gz,fastq fastq,9307586160.0,77563218.0,GSM6062264 r3,0:29 1:91,A:2569072609;C:2102732051;G:2247036264;T:2388393636;N:351600,29,91,,,2569072609,2102732051,2247036264,2388393636,351600,SRX14979859,SRS12729750,SRA1408865,"Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center","Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.00429,0.87889,0.00178,0.1429,0.99271,0.78589,0.35728,0.54587,29,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-04-23,Undetermined,Undetermined,Skin,Surface Structure
69561,SRR18901605,SRX14979859,SRS12729750,SRP371883,PRJNA831276,Lipid droplets are a metabolic vulnerability in melanoma,GSE201378,Transcriptome Analysis,Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma,,pubmed:37268606,,TEAZ scRNAseq,GSM6062264,,source name:Skin|tissue:Skin|cell type:melanoma,TEAZ scRNAseq,Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11,Skin,,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,tissue:Skin|cell type:melanoma,GSM6062264,GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq,GSM6062264 r1,GSM6062264,1,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,loader:fastq load.py,2544_PTEN_combined_IGO_11963_4_S2_L004_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L004_R2_001.fastq.gz,fastq fastq,9382270920.0,78185591.0,GSM6062264 r4,0:29 1:91,A:2591803792;C:2116313097;G:2264892157;T:2408930364;N:331510,29,91,,,2591803792,2116313097,2264892157,2408930364,331510,SRX14979859,SRS12729750,SRA1408865,"Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center","Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.00445,0.87912,0.00184,0.14625,0.99287,0.78573,0.37029,0.5207,29,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-04-23,Undetermined,Undetermined,Skin,Surface Structure
70092,SRR24739157,SRX20516499,SRS17826365,SRP377666,PRJNA843735,Alpha 1 adrenergic signaling drives cardiac regeneration through activation of extracellular matrix remodeling transcriptional program in macrophages,GSE205103,Transcriptome Analysis,Autonomic drive plays a pivotal role in cardiac regeneration. Sympathetic or cholinergic denervation impairs myocardial regrowth in neonatal mouse and zebrafish hearts. Here  we uncovered the mechanistic underpinning of adrenergic signaling in regenerative repair of the heart to be critically dependent on immunomodulation. Through pharmacological and genetic manipulations  we identified adrenergic receptor alpha 1 as a key regulator of macrophage phenotypic diversification following myocardial infarction in zebrafish. Single cell transcriptomics revealed that the receptor signals activation of an 'extracellular matrix remodeling' transcriptional program characterized by upregulation of matrix proteins and matrix modifying enzymes in a macrophage subset. Functionally  adrenergic receptor alpha 1 activated macrophages regulate fibrotic response of the heart by mediating collagenous extracellular matrix turnover and myofibroblast activation  allowing vascularization and cardiomyocyte cell cycle entry at the infarcted lesion. These findings not only unravel the mechanism of adrenergic signaling in macrophage phenotypic and functional determination  but also highlight the potential of neural modulation for regulation of fibrosis and coordination of myocardial regenerative response. Overall design: Zebrafish hearts subjected to cryoinjury were collected at 7 dpi  dissociated and live cells  sorted by FACS  analyzed with scRNAseq,,pubmed:37875117,,control heart  cryoinjured,GSM7427915,,source name:heart|strain:AB/TU|time:7 xxx post injury|tissue:heart|genotype:TgBACcsf1ra:GAL4 VP16i186; TgUAS:NTR mCherryc264|treatment:cryoinjury|geo loc name:missing|collection date:missing,control heart  cryoinjured,the steps until acquiring the fastq files demultiplexing  conversion to fastq were done by the Genomics technology platform in Max Delbruck Centrum. Then Cell Ranger software v6.0.1 was used for counting  alignment with the fastq files. https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger then Seu Assembly: GRCz11 release 104 Supplementary files format and content: Tab separated values files and matrix files,heart,,zebrafish with TgBACcsf1ra:GAL4 VP16i186; TgUAS:NTR mCherryc264  transgenes subjected to cryoinjury and hearts were collected at 7 dpi and transferred into dissociation solution containing 0.26 U/ml LiberaseTM enzyme mixture Sigma and 1X Pluronic F 68 ThermoFisher in HBSS. Hearts were incubated in dissociation solution for 30 minutes with shaking at 750 rpm at 37°C with intermittent pipetting every 5 minutes. Live cells were sorted by FACS. Library was constructed according to the manufacterer’s instructions of Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry. library preparation was done by Genomics technology platform in Max Delbruck Centrum,,strain:AB/TU|time:7 xxx post injury|tissue:heart|genotype:TgBACcsf1ra:GAL4 VP16i186; TgUAS:NTR mCherryc264|treatment:cryoinjury,GSM7427915,GSM7427915: control heart  cryoinjured; Danio rerio; RNA Seq,GSM7427915 r1,GSM7427915,1,zebrafish with TgBACcsf1ra:GAL4 VP16i186; TgUAS:NTR mCherryc264  transgenes subjected to cryoinjury and hearts were collected at 7 dpi and transferred into dissociation solution containing 0.26 U/ml LiberaseTM enzyme mixture Sigma and 1X Pluronic F 68 ThermoFisher in HBSS. Hearts were incubated in dissociation solution for 30 minutes with shaking at 750 rpm at 37°C with intermittent pipetting every 5 minutes. Live cells were sorted by FACS. Library was constructed according to the manufacterer's instructions of Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry. library preparation was done by Genomics technology platform in Max Delbruck Centrum,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP377666,,loader:fastq load.py,P1792_SP106_009_S1_L001_R1_001.fastq.gz P1792_SP106_009_S1_L001_R2_001.fastq.gz,fastq fastq,44106695018.0,373785551.0,GSM7427915 r1,0:28 1:90,A:11119116130;C:11277976932;G:10463548412;T:11244752649;N:1300895,28,90,,,11119116130,11277976932,10463548412,11244752649,1300895,SRX20516499,SRS17826365,SRA1644267,Max Delbruck Centrum,Max Delbruck Centrum,2,0.00282,0.92876,0.0008,0.04739,0.99669,0.89246,0.3378,0.50554,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-05-25,Undetermined,Undetermined,Heart,Cardiovascular System
70093,SRR19448659,SRX15501759,SRS13216610,SRP377666,PRJNA843735,Alpha 1 adrenergic signaling drives cardiac regeneration through activation of extracellular matrix remodeling transcriptional program in macrophages,GSE205103,Transcriptome Analysis,Autonomic drive plays a pivotal role in cardiac regeneration. Sympathetic or cholinergic denervation impairs myocardial regrowth in neonatal mouse and zebrafish hearts. Here  we uncovered the mechanistic underpinning of adrenergic signaling in regenerative repair of the heart to be critically dependent on immunomodulation. Through pharmacological and genetic manipulations  we identified adrenergic receptor alpha 1 as a key regulator of macrophage phenotypic diversification following myocardial infarction in zebrafish. Single cell transcriptomics revealed that the receptor signals activation of an 'extracellular matrix remodeling' transcriptional program characterized by upregulation of matrix proteins and matrix modifying enzymes in a macrophage subset. Functionally  adrenergic receptor alpha 1 activated macrophages regulate fibrotic response of the heart by mediating collagenous extracellular matrix turnover and myofibroblast activation  allowing vascularization and cardiomyocyte cell cycle entry at the infarcted lesion. These findings not only unravel the mechanism of adrenergic signaling in macrophage phenotypic and functional determination  but also highlight the potential of neural modulation for regulation of fibrosis and coordination of myocardial regenerative response. Overall design: Zebrafish hearts subjected to cryoinjury were collected at 7 dpi  dissociated and live cells  sorted by FACS  analyzed with scRNAseq,,pubmed:37875117,,heart  cryoinjured,GSM6205275,,source name:heart|strain:AB/TU|time:7 xxx post injury|tissue:heart|genotype:TgBACcsf1ra:GAL4 VP16i186; TgUAS:NTR mCherryc264; TgUAS:adra1 3i T2A CFP|treatment:cryoinjury|geo loc name:missing|collection date:missing,heart  cryoinjured,the steps until acquiring the fastq files demultiplexing  conversion to fastq were done by the Genomics technology platform in Max Delbruck Centrum. Then Cell Ranger software v6.0.1 was used for counting  alignment with the fastq files. https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger then Seu Assembly: GRCz11 release 104 Supplementary files format and content: Tab separated values files and matrix files,heart,,zebrafish with TgBACcsf1ra:GAL4 VP16i186; TgUAS:NTR mCherryc264; TgUAS:adra1 3i T2A CFP transgenes subjected to cryoinjury and hearts were collected at 7 dpi and transferred into dissociation solution containing 0.26 U/ml LiberaseTM enzyme mixture Sigma and 1X Pluronic F 68 ThermoFisher in HBSS. Hearts were incubated in dissociation solution for 30 minutes with shaking at 750 rpm at 37°C with intermittent pipetting every 5 minutes. Live cells were sorted by FACS. Library was constructed according to the manufacterer’s instructions of Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry. library preparation was done by Genomics technology platform in Max Delbruck Centrum,,strain:AB/TU|time:7 xxx post injury|tissue:heart|genotype:TgBACcsf1ra:GAL4 VP16i186; TgUAS:NTR mCherryc264; TgUAS:adra1 3i T2A CFP|treatment:cryoinjury,GSM6205275,GSM6205275: heart  cryoinjured; Danio rerio; RNA Seq,GSM6205275 r1,GSM6205275,1,zebrafish with TgBACcsf1ra:GAL4 VP16i186; TgUAS:NTR mCherryc264; TgUAS:adra1 3i T2A CFP transgenes subjected to cryoinjury and hearts were collected at 7 dpi and transferred into dissociation solution containing 0.26 U/ml LiberaseTM enzyme mixture Sigma and 1X Pluronic F 68 ThermoFisher in HBSS. Hearts were incubated in dissociation solution for 30 minutes with shaking at 750 rpm at 37°C with intermittent pipetting every 5 minutes. Live cells were sorted by FACS. Library was constructed according to the manufacterer's instructions of Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry. library preparation was done by Genomics technology platform in Max Delbruck Centrum,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP377666,,loader:fastq load.py,SP106_006_S1_L001_I1_001.fastq.gz SP106_006_S1_L001_I2_001.fastq.gz SP106_006_S1_L001_R1_001.fastq.gz SP106_006_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,65403269016.0,473936732.0,GSM6205275 r1,0:10 1:10 2:28 3:90,A:11749384482;C:10044369062;G:10233374754;T:10627004245;N:173337,10,10,28,90,11749384482,10044369062,10233374754,10627004245,173337,SRX15501759,SRS13216610,SRA1428956,Max Delbruck Centrum,Max Delbruck Centrum,1,0.94557,,0.09314,,0.83652,,0.52678,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2022-05-30,Undetermined,Undetermined,Heart,Cardiovascular System
71397,SRR21571181,SRX17573445,SRS15113179,SRP397130,PRJNA880596,A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq],GSE213359,Transcriptome Analysis,Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response  while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler  SATB2  which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed  1 MCR:SATB2 tumor expressing TIE:EGFP was processed,parent bioproject:PRJNA880593,,,TIE:EGFP MCR:MCS Tumor 2 GFP+ #3,GSM6580971,,source name:MCR:MCS Melanoma|tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+|geo loc name:missing|collection date:missing,TIE:EGFP MCR:MCS Tumor 2 GFP+ #3,The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator  following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed  and aligned to zebrafish reference genome GRCz11 using Rsubread  and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv,MCR:MCS Melanoma,Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,N/A,tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+,GSM6580971,GSM6580971: TIE:EGFP MCR:MCS Tumor 2 GFP+ #3; Danio rerio; RNA Seq,GSM6580971 r1,GSM6580971,1,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP397130,,,HAR-HN-s014.R1.fastq.gz HAR-HN-s014.R2.fastq.gz,fastq fastq,2393526200.0,27831700.0,GSM6580971 r1,0:26 1:60,A:587629810;C:436040251;G:440163052;T:929430783;N:262304,26,60,,,587629810,436040251,440163052,929430783,262304,SRX17573445,SRS15113179,,,"Oncology/Hematology, Boston Children's Hospital",2,0.1102,0.89036,0.10359,0.25006,0.99285,0.81172,0.56209,0.58312,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2022-09-14,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
71398,SRR21571182,SRX17573444,SRS15113178,SRP397130,PRJNA880596,A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq],GSE213359,Transcriptome Analysis,Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response  while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler  SATB2  which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed  1 MCR:SATB2 tumor expressing TIE:EGFP was processed,parent bioproject:PRJNA880593,,,TIE:EGFP MCR:MCS Tumor 2 GFP /mCherry+,GSM6580970,,source name:MCR:MCS Melanoma|tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP /mCherry+|geo loc name:missing|collection date:missing,TIE:EGFP MCR:MCS Tumor 2 GFP /mCherry+,The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator  following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed  and aligned to zebrafish reference genome GRCz11 using Rsubread  and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv,MCR:MCS Melanoma,Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,N/A,tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP /mCherry+,GSM6580970,GSM6580970: TIE:EGFP MCR:MCS Tumor 2 GFP /mCherry+; Danio rerio; RNA Seq,GSM6580970 r1,GSM6580970,1,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP397130,,,HAR-HN-s013.R1.fastq.gz HAR-HN-s013.R2.fastq.gz,fastq fastq,2799404318.0,32551213.0,GSM6580970 r1,0:26 1:60,A:674562015;C:518279489;G:507732521;T:1093251404;N:5578889,26,60,,,674562015,518279489,507732521,1093251404,5578889,SRX17573444,SRS15113178,,,"Oncology/Hematology, Boston Children's Hospital",2,0.11385,0.89818,0.10608,0.24805,0.99162,0.80519,0.57833,0.58452,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2022-09-14,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
71399,SRR21571183,SRX17573443,SRS15113177,SRP397130,PRJNA880596,A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq],GSE213359,Transcriptome Analysis,Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response  while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler  SATB2  which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed  1 MCR:SATB2 tumor expressing TIE:EGFP was processed,parent bioproject:PRJNA880593,,,TIE:EGFP MCR:MCS Tumor 2 GFP+ #2,GSM6580969,,source name:MCR:MCS Melanoma|tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+|geo loc name:missing|collection date:missing,TIE:EGFP MCR:MCS Tumor 2 GFP+ #2,The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator  following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed  and aligned to zebrafish reference genome GRCz11 using Rsubread  and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv,MCR:MCS Melanoma,Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,N/A,tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+,GSM6580969,GSM6580969: TIE:EGFP MCR:MCS Tumor 2 GFP+ #2; Danio rerio; RNA Seq,GSM6580969 r1,GSM6580969,1,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP397130,,,HAR-HN-s012.R1.fastq.gz HAR-HN-s012.R2.fastq.gz,fastq fastq,2643515042.0,30738547.0,GSM6580969 r1,0:26 1:60,A:644064543;C:487933120;G:466421088;T:1039827853;N:5268438,26,60,,,644064543,487933120,466421088,1039827853,5268438,SRX17573443,SRS15113177,,,"Oncology/Hematology, Boston Children's Hospital",2,0.11114,0.8924,0.10417,0.25808,0.99151,0.80499,0.60121,0.567,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2022-09-14,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
71400,SRR21571184,SRX17573442,SRS15113176,SRP397130,PRJNA880596,A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq],GSE213359,Transcriptome Analysis,Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response  while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler  SATB2  which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed  1 MCR:SATB2 tumor expressing TIE:EGFP was processed,parent bioproject:PRJNA880593,,,TIE:EGFP MCR:MCS Tumor 2 GFP+ #1,GSM6580968,,source name:MCR:MCS Melanoma|tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+|geo loc name:missing|collection date:missing,TIE:EGFP MCR:MCS Tumor 2 GFP+ #1,The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator  following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed  and aligned to zebrafish reference genome GRCz11 using Rsubread  and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv,MCR:MCS Melanoma,Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,N/A,tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+,GSM6580968,GSM6580968: TIE:EGFP MCR:MCS Tumor 2 GFP+ #1; Danio rerio; RNA Seq,GSM6580968 r1,GSM6580968,1,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP397130,,,HAR-HN-s011.R1.fastq.gz HAR-HN-s011.R2.fastq.gz,fastq fastq,2701784858.0,31416103.0,GSM6580968 r1,0:26 1:60,A:654129800;C:498352764;G:495215316;T:1048678271;N:5408707,26,60,,,654129800,498352764,495215316,1048678271,5408707,SRX17573442,SRS15113176,,,"Oncology/Hematology, Boston Children's Hospital",2,0.10435,0.89555,0.0971,0.26327,0.99354,0.80647,0.56789,0.50648,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2022-09-14,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
71401,SRR21571185,SRX17573441,SRS15113175,SRP397130,PRJNA880596,A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq],GSE213359,Transcriptome Analysis,Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response  while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler  SATB2  which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed  1 MCR:SATB2 tumor expressing TIE:EGFP was processed,parent bioproject:PRJNA880593,,,TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #3,GSM6580967,,source name:MCR:SATB2 Melanoma|tissue:MCR:SATB2 Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+|geo loc name:missing|collection date:missing,TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #3,The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator  following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed  and aligned to zebrafish reference genome GRCz11 using Rsubread  and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv,MCR:SATB2 Melanoma,Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,N/A,tissue:MCR:SATB2 Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+,GSM6580967,GSM6580967: TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #3; Danio rerio; RNA Seq,GSM6580967 r1,GSM6580967,1,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP397130,,,HAR-HN-s007.R1.fastq.gz HAR-HN-s007.R2.fastq.gz,fastq fastq,3169503770.0,36854695.0,GSM6580967 r1,0:26 1:60,A:758395203;C:580012810;G:565741250;T:1265023729;N:330778,26,60,,,758395203,580012810,565741250,1265023729,330778,SRX17573441,SRS15113175,,,"Oncology/Hematology, Boston Children's Hospital",2,0.11903,0.89395,0.11159,0.29218,0.99243,0.79705,0.54327,0.56983,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2022-09-14,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
71402,SRR21571186,SRX17573440,SRS15113174,SRP397130,PRJNA880596,A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq],GSE213359,Transcriptome Analysis,Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response  while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler  SATB2  which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed  1 MCR:SATB2 tumor expressing TIE:EGFP was processed,parent bioproject:PRJNA880593,,,TIE:EGFP MCR:SATB2 Tumor 1 GFP /mCherry+,GSM6580966,,source name:MCR:SATB2 Melanoma|tissue:MCR:SATB2 Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP /mCherry+|geo loc name:missing|collection date:missing,TIE:EGFP MCR:SATB2 Tumor 1 GFP /mCherry+,The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator  following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed  and aligned to zebrafish reference genome GRCz11 using Rsubread  and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv,MCR:SATB2 Melanoma,Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,N/A,tissue:MCR:SATB2 Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP /mCherry+,GSM6580966,GSM6580966: TIE:EGFP MCR:SATB2 Tumor 1 GFP /mCherry+; Danio rerio; RNA Seq,GSM6580966 r1,GSM6580966,1,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP397130,,,HAR-HN-s006.R1.fastq.gz HAR-HN-s006.R2.fastq.gz,fastq fastq,3401223030.0,39549105.0,GSM6580966 r1,0:26 1:60,A:811721089;C:634467013;G:610447766;T:1344233621;N:353541,26,60,,,811721089,634467013,610447766,1344233621,353541,SRX17573440,SRS15113174,,,"Oncology/Hematology, Boston Children's Hospital",2,0.11728,0.9042,0.11084,0.22711,0.9931,0.79494,0.65306,0.56756,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2022-09-14,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
71403,SRR21571187,SRX17573439,SRS15113173,SRP397130,PRJNA880596,A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq],GSE213359,Transcriptome Analysis,Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response  while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler  SATB2  which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed  1 MCR:SATB2 tumor expressing TIE:EGFP was processed,parent bioproject:PRJNA880593,,,TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #2,GSM6580965,,source name:MCR:SATB2 Melanoma|tissue:MCR:SATB2 Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+|geo loc name:missing|collection date:missing,TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #2,The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator  following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed  and aligned to zebrafish reference genome GRCz11 using Rsubread  and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv,MCR:SATB2 Melanoma,Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,N/A,tissue:MCR:SATB2 Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+,GSM6580965,GSM6580965: TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #2; Danio rerio; RNA Seq,GSM6580965 r1,GSM6580965,1,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP397130,,,HAR-HN-s005.R1.fastq.gz HAR-HN-s005.R2.fastq.gz,fastq fastq,3042431718.0,35377113.0,GSM6580965 r1,0:26 1:60,A:744782141;C:565144430;G:541953297;T:1190237432;N:314418,26,60,,,744782141,565144430,541953297,1190237432,314418,SRX17573439,SRS15113173,,,"Oncology/Hematology, Boston Children's Hospital",2,0.11149,0.88671,0.10471,0.23988,0.99162,0.79543,0.64395,0.58192,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2022-09-14,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
71404,SRR21571188,SRX17573438,SRS15113172,SRP397130,PRJNA880596,A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq],GSE213359,Transcriptome Analysis,Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response  while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler  SATB2  which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed  1 MCR:SATB2 tumor expressing TIE:EGFP was processed,parent bioproject:PRJNA880593,,,TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #1,GSM6580964,,source name:MCR:SATB2 Melanoma|tissue:MCR:SATB2 Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+|geo loc name:missing|collection date:missing,TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #1,The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator  following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed  and aligned to zebrafish reference genome GRCz11 using Rsubread  and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv,MCR:SATB2 Melanoma,Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,N/A,tissue:MCR:SATB2 Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+,GSM6580964,GSM6580964: TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #1; Danio rerio; RNA Seq,GSM6580964 r1,GSM6580964,1,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP397130,,,HAR-HN-s004.R1.fastq.gz HAR-HN-s004.R2.fastq.gz,fastq fastq,3454727328.0,40171248.0,GSM6580964 r1,0:26 1:60,A:823342460;C:630914117;G:615200919;T:1384911330;N:358502,26,60,,,823342460,630914117,615200919,1384911330,358502,SRX17573438,SRS15113172,,,"Oncology/Hematology, Boston Children's Hospital",2,0.12493,0.8892,0.11706,0.21947,0.99314,0.79216,0.73215,0.53614,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2022-09-14,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
71405,SRR21571189,SRX17573437,SRS15113171,SRP397130,PRJNA880596,A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq],GSE213359,Transcriptome Analysis,Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response  while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler  SATB2  which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed  1 MCR:SATB2 tumor expressing TIE:EGFP was processed,parent bioproject:PRJNA880593,,,TIE:EGFP MCR:MCS Tumor 1 GFP+ #3,GSM6580963,,source name:MCR:MCS Melanoma|tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+|geo loc name:missing|collection date:missing,TIE:EGFP MCR:MCS Tumor 1 GFP+ #3,The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator  following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed  and aligned to zebrafish reference genome GRCz11 using Rsubread  and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv,MCR:MCS Melanoma,Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,N/A,tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+,GSM6580963,GSM6580963: TIE:EGFP MCR:MCS Tumor 1 GFP+ #3; Danio rerio; RNA Seq,GSM6580963 r1,GSM6580963,1,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP397130,,,HAR-SW-s016.R1.fastq.gz HAR-SW-s016.R2.fastq.gz,fastq fastq,2986527160.0,34727060.0,GSM6580963 r1,0:26 1:60,A:741435297;C:548375629;G:534147329;T:1162130158;N:438747,26,60,,,741435297,548375629,534147329,1162130158,438747,SRX17573437,SRS15113171,,,"Oncology/Hematology, Boston Children's Hospital",2,0.12032,0.87963,0.11182,0.30887,0.99145,0.79926,0.53199,0.59453,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2022-09-14,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
71406,SRR21571190,SRX17573436,SRS15113170,SRP397130,PRJNA880596,A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq],GSE213359,Transcriptome Analysis,Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response  while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler  SATB2  which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed  1 MCR:SATB2 tumor expressing TIE:EGFP was processed,parent bioproject:PRJNA880593,,,TIE:EGFP MCR:MCS Tumor 1 mCherry+;GFP ,GSM6580962,,source name:MCR:MCS Melanoma|tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:mCherry+;GFP |geo loc name:missing|collection date:missing,TIE:EGFP MCR:MCS Tumor 1 mCherry+;GFP ,The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator  following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed  and aligned to zebrafish reference genome GRCz11 using Rsubread  and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv,MCR:MCS Melanoma,Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,N/A,tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:mCherry+;GFP ,GSM6580962,GSM6580962: TIE:EGFP MCR:MCS Tumor 1 mCherry+;GFP ; Danio rerio; RNA Seq,GSM6580962 r1,GSM6580962,1,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP397130,,,HAR-SW-s015.R1.fastq.gz HAR-SW-s015.R2.fastq.gz,fastq fastq,2668318990.0,31026965.0,GSM6580962 r1,0:26 1:60,A:650521761;C:486885070;G:465311971;T:1065210518;N:389670,26,60,,,650521761,486885070,465311971,1065210518,389670,SRX17573436,SRS15113170,,,"Oncology/Hematology, Boston Children's Hospital",2,0.1142,0.88526,0.10718,0.34648,0.99198,0.80428,0.56024,0.56437,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2022-09-14,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
71407,SRR21571191,SRX17573435,SRS15113168,SRP397130,PRJNA880596,A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq],GSE213359,Transcriptome Analysis,Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response  while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler  SATB2  which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed  1 MCR:SATB2 tumor expressing TIE:EGFP was processed,parent bioproject:PRJNA880593,,,TIE:EGFP MCR:MCS Tumor 1 GFP+ #2,GSM6580961,,source name:MCR:MCS Melanoma|tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+|geo loc name:missing|collection date:missing,TIE:EGFP MCR:MCS Tumor 1 GFP+ #2,The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator  following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed  and aligned to zebrafish reference genome GRCz11 using Rsubread  and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv,MCR:MCS Melanoma,Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,N/A,tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+,GSM6580961,GSM6580961: TIE:EGFP MCR:MCS Tumor 1 GFP+ #2; Danio rerio; RNA Seq,GSM6580961 r1,GSM6580961,1,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP397130,,,HAR-SW-s014.R1.fastq.gz HAR-SW-s014.R2.fastq.gz,fastq fastq,2393946138.0,27836583.0,GSM6580961 r1,0:26 1:60,A:596410784;C:437801560;G:418907527;T:940499589;N:326678,26,60,,,596410784,437801560,418907527,940499589,326678,SRX17573435,SRS15113168,,,"Oncology/Hematology, Boston Children's Hospital",2,0.12342,0.85959,0.11689,0.34528,0.98965,0.80472,0.49199,0.56661,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2022-09-14,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
71408,SRR21571192,SRX17573434,SRS15113169,SRP397130,PRJNA880596,A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq],GSE213359,Transcriptome Analysis,Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response  while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler  SATB2  which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed  1 MCR:SATB2 tumor expressing TIE:EGFP was processed,parent bioproject:PRJNA880593,,,TIE:EGFP MCR:MCS Tumor 1 GFP+ #1,GSM6580960,,source name:MCR:MCS Melanoma|tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+|geo loc name:missing|collection date:missing,TIE:EGFP MCR:MCS Tumor 1 GFP+ #1,The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator  following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed  and aligned to zebrafish reference genome GRCz11 using Rsubread  and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv,MCR:MCS Melanoma,Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,N/A,tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+,GSM6580960,GSM6580960: TIE:EGFP MCR:MCS Tumor 1 GFP+ #1; Danio rerio; RNA Seq,GSM6580960 r1,GSM6580960,1,Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP397130,,,HAR-SW-s013.R1.fastq.gz HAR-SW-s013.R2.fastq.gz,fastq fastq,3043161084.0,35385594.0,GSM6580960 r1,0:26 1:60,A:750431276;C:555809857;G:537628053;T:1198847837;N:444061,26,60,,,750431276,555809857,537628053,1198847837,444061,SRX17573434,SRS15113169,,,"Oncology/Hematology, Boston Children's Hospital",2,0.11034,0.86528,0.10371,0.32665,0.99198,0.79695,0.51927,0.58318,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2022-09-14,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
73951,SRR23290994,SRX19234275,SRS16638733,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 21dpi 2,GSM7016815,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing,zfCM 21dpi 2,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi,GSM7016815,GSM7016815: zfCM 21dpi 2; Danio rerio; RNA Seq,GSM7016815 r1,GSM7016815,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-s041_H7L35BGXM_S4_L001_R1_001.fastq.gz HUB-PN-s041_H7L35BGXM_S4_L001_R2_001.fastq.gz,fastq fastq,858173876.0,9978766.0,GSM7016815 r1,0:26 1:60,A:213059809;C:160771814;G:156105199;T:328218073;N:18981,26,60,,,213059809,160771814,156105199,328218073,18981,SRX19234275,SRS16638733,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11426,0.88222,0.10668,0.29657,0.99149,0.8355,0.60863,0.67263,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73952,SRR23290995,SRX19234275,SRS16638733,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 21dpi 2,GSM7016815,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing,zfCM 21dpi 2,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi,GSM7016815,GSM7016815: zfCM 21dpi 2; Danio rerio; RNA Seq,GSM7016815 r1,GSM7016815,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-s041_H7L35BGXM_S4_L002_R1_001.fastq.gz HUB-PN-s041_H7L35BGXM_S4_L002_R2_001.fastq.gz,fastq fastq,843721318.0,9810713.0,GSM7016815 r2,0:26 1:60,A:208714473;C:157371099;G:155893107;T:321724427;N:18212,26,60,,,208714473,157371099,155893107,321724427,18212,SRX19234275,SRS16638733,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11232,0.8799,0.10497,0.29809,0.99123,0.83621,0.66836,0.66521,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73953,SRR23290996,SRX19234275,SRS16638733,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 21dpi 2,GSM7016815,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing,zfCM 21dpi 2,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi,GSM7016815,GSM7016815: zfCM 21dpi 2; Danio rerio; RNA Seq,GSM7016815 r1,GSM7016815,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-s041_H7L35BGXM_S4_L003_R1_001.fastq.gz HUB-PN-s041_H7L35BGXM_S4_L003_R2_001.fastq.gz,fastq fastq,864128860.0,10048010.0,GSM7016815 r3,0:26 1:60,A:214256028;C:161957471;G:157308166;T:330585259;N:21936,26,60,,,214256028,161957471,157308166,330585259,21936,SRX19234275,SRS16638733,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.1147,0.88514,0.10704,0.29827,0.99105,0.83321,0.67314,0.65637,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73954,SRR23290997,SRX19234275,SRS16638733,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 21dpi 2,GSM7016815,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing,zfCM 21dpi 2,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi,GSM7016815,GSM7016815: zfCM 21dpi 2; Danio rerio; RNA Seq,GSM7016815 r1,GSM7016815,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-s041_H7L35BGXM_S4_L004_R1_001.fastq.gz HUB-PN-s041_H7L35BGXM_S4_L004_R2_001.fastq.gz,fastq fastq,862094960.0,10024360.0,GSM7016815 r4,0:26 1:60,A:212975380;C:160923939;G:159237695;T:328939876;N:18070,26,60,,,212975380,160923939,159237695,328939876,18070,SRX19234275,SRS16638733,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11191,0.88105,0.10467,0.2945,0.99151,0.83623,0.67428,0.67156,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73955,SRR23290998,SRX19234274,SRS16638732,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 4,GSM7016814,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 4,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016814,GSM7016814: zfCM 7dpi 4; Danio rerio; RNA Seq,GSM7016814 r1,GSM7016814,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-s039_H7L35BGXM_S3_L001_R1_001.fastq.gz HUB-PN-s039_H7L35BGXM_S3_L001_R2_001.fastq.gz,fastq fastq,839750096.0,9764536.0,GSM7016814 r1,0:26 1:60,A:207245393;C:152642612;G:152075698;T:327767742;N:18651,26,60,,,207245393,152642612,152075698,327767742,18651,SRX19234274,SRS16638732,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10807,0.88063,0.1011,0.31218,0.99133,0.81844,0.57963,0.58371,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73956,SRR23290999,SRX19234274,SRS16638732,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 4,GSM7016814,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 4,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016814,GSM7016814: zfCM 7dpi 4; Danio rerio; RNA Seq,GSM7016814 r1,GSM7016814,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-s039_H7L35BGXM_S3_L002_R1_001.fastq.gz HUB-PN-s039_H7L35BGXM_S3_L002_R2_001.fastq.gz,fastq fastq,824555530.0,9587855.0,GSM7016814 r2,0:26 1:60,A:202762477;C:149247401;G:151695233;T:320832302;N:18117,26,60,,,202762477,149247401,151695233,320832302,18117,SRX19234274,SRS16638732,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10764,0.87478,0.1005,0.31049,0.99101,0.81929,0.58127,0.51321,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73957,SRR23291000,SRX19234274,SRS16638732,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 4,GSM7016814,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 4,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016814,GSM7016814: zfCM 7dpi 4; Danio rerio; RNA Seq,GSM7016814 r1,GSM7016814,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-s039_H7L35BGXM_S3_L003_R1_001.fastq.gz HUB-PN-s039_H7L35BGXM_S3_L003_R2_001.fastq.gz,fastq fastq,845111766.0,9826881.0,GSM7016814 r3,0:26 1:60,A:208286833;C:153694024;G:153159692;T:329951816;N:19401,26,60,,,208286833,153694024,153159692,329951816,19401,SRX19234274,SRS16638732,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.1087,0.88111,0.10148,0.31291,0.99068,0.81698,0.55014,0.58727,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73958,SRR23291001,SRX19234274,SRS16638732,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 4,GSM7016814,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 4,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016814,GSM7016814: zfCM 7dpi 4; Danio rerio; RNA Seq,GSM7016814 r1,GSM7016814,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-s039_H7L35BGXM_S3_L004_R1_001.fastq.gz HUB-PN-s039_H7L35BGXM_S3_L004_R2_001.fastq.gz,fastq fastq,842710216.0,9798956.0,GSM7016814 r4,0:26 1:60,A:206896294;C:152644705;G:155014140;T:328138108;N:16969,26,60,,,206896294,152644705,155014140,328138108,16969,SRX19234274,SRS16638732,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10766,0.87731,0.10058,0.31053,0.99119,0.81781,0.57185,0.57715,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73959,SRR23291002,SRX19234273,SRS16638731,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 21dpi 1,GSM7016813,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing,zfCM 21dpi 1,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi,GSM7016813,GSM7016813: zfCM 21dpi 1; Danio rerio; RNA Seq,GSM7016813 r1,GSM7016813,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-025_HCMYKBGXC_S8_L001_R1_001.fastq.gz HUB-PN-025_HCMYKBGXC_S8_L001_R2_001.fastq.gz,fastq fastq,638322358.0,7422353.0,GSM7016813 r1,0:26 1:60,A:152993677;C:129279491;G:116490423;T:238075133;N:1483634,26,60,,,152993677,129279491,116490423,238075133,1483634,SRX19234273,SRS16638731,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.1186,0.92133,0.11281,0.53473,0.99391,0.89818,0.6282,0.56941,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73960,SRR23291003,SRX19234273,SRS16638731,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 21dpi 1,GSM7016813,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing,zfCM 21dpi 1,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi,GSM7016813,GSM7016813: zfCM 21dpi 1; Danio rerio; RNA Seq,GSM7016813 r1,GSM7016813,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-025_HCMYKBGXC_S8_L002_R1_001.fastq.gz HUB-PN-025_HCMYKBGXC_S8_L002_R2_001.fastq.gz,fastq fastq,633345022.0,7364477.0,GSM7016813 r2,0:26 1:60,A:150874121;C:127629476;G:118171343;T:235389766;N:1280316,26,60,,,150874121,127629476,118171343,235389766,1280316,SRX19234273,SRS16638731,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11665,0.91596,0.11139,0.53318,0.99425,0.89822,0.64949,0.56009,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73961,SRR23291004,SRX19234273,SRS16638731,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 21dpi 1,GSM7016813,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing,zfCM 21dpi 1,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi,GSM7016813,GSM7016813: zfCM 21dpi 1; Danio rerio; RNA Seq,GSM7016813 r1,GSM7016813,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-025_HCMYKBGXC_S8_L003_R1_001.fastq.gz HUB-PN-025_HCMYKBGXC_S8_L003_R2_001.fastq.gz,fastq fastq,643723416.0,7485156.0,GSM7016813 r3,0:26 1:60,A:154277144;C:130529094;G:117635488;T:240275453;N:1006237,26,60,,,154277144,130529094,117635488,240275453,1006237,SRX19234273,SRS16638731,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11809,0.9216,0.11258,0.53566,0.99397,0.89871,0.63435,0.55308,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73962,SRR23291005,SRX19234273,SRS16638731,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 21dpi 1,GSM7016813,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing,zfCM 21dpi 1,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi,GSM7016813,GSM7016813: zfCM 21dpi 1; Danio rerio; RNA Seq,GSM7016813 r1,GSM7016813,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-025_HCMYKBGXC_S8_L004_R1_001.fastq.gz HUB-PN-025_HCMYKBGXC_S8_L004_R2_001.fastq.gz,fastq fastq,632759362.0,7357667.0,GSM7016813 r4,0:26 1:60,A:150797181;C:127674217;G:117974605;T:235361625;N:951734,26,60,,,150797181,127674217,117974605,235361625,951734,SRX19234273,SRS16638731,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11662,0.91609,0.11147,0.53237,0.99381,0.89775,0.65781,0.55524,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73963,SRR23291006,SRX19234272,SRS16638730,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 3,GSM7016812,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 3,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016812,GSM7016812: zfCM 7dpi 3; Danio rerio; RNA Seq,GSM7016812 r1,GSM7016812,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-DB-006_HNWVVBGX9_S5_L001_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L001_R2_001.fastq.gz,fastq fastq,929999528.0,10813948.0,GSM7016812 r1,0:26 1:60,A:240334465;C:174255952;G:184260587;T:330943403;N:205121,26,60,,,240334465,174255952,184260587,330943403,205121,SRX19234272,SRS16638730,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11116,0.87404,0.10307,0.43901,0.99178,0.93034,0.6268,0.44639,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73964,SRR23291007,SRX19234272,SRS16638730,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 3,GSM7016812,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 3,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016812,GSM7016812: zfCM 7dpi 3; Danio rerio; RNA Seq,GSM7016812 r1,GSM7016812,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-DB-006_HNWVVBGX9_S5_L002_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L002_R2_001.fastq.gz,fastq fastq,987824896.0,11486336.0,GSM7016812 r2,0:26 1:60,A:251121714;C:184449811;G:201317783;T:350692225;N:243363,26,60,,,251121714,184449811,201317783,350692225,243363,SRX19234272,SRS16638730,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11269,0.87873,0.10426,0.44461,0.99172,0.92506,0.6241,0.4506,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73965,SRR23291008,SRX19234272,SRS16638730,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 3,GSM7016812,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 3,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016812,GSM7016812: zfCM 7dpi 3; Danio rerio; RNA Seq,GSM7016812 r1,GSM7016812,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-DB-006_HNWVVBGX9_S5_L003_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L003_R2_001.fastq.gz,fastq fastq,959933032.0,11162012.0,GSM7016812 r3,0:26 1:60,A:247983556;C:179564753;G:190342582;T:341858456;N:183685,26,60,,,247983556,179564753,190342582,341858456,183685,SRX19234272,SRS16638730,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11176,0.87161,0.10342,0.43986,0.99155,0.93026,0.63442,0.44405,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73966,SRR23291009,SRX19234272,SRS16638730,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 3,GSM7016812,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 3,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016812,GSM7016812: zfCM 7dpi 3; Danio rerio; RNA Seq,GSM7016812 r1,GSM7016812,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-DB-006_HNWVVBGX9_S5_L004_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L004_R2_001.fastq.gz,fastq fastq,798370766.0,9283381.0,GSM7016812 r4,0:26 1:60,A:205538880;C:148510556;G:161196381;T:282964175;N:160774,26,60,,,205538880,148510556,161196381,282964175,160774,SRX19234272,SRS16638730,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11014,0.87018,0.10209,0.43668,0.9921,0.93346,0.56645,0.44683,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73967,SRR23291010,SRX19234271,SRS16638729,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 2,GSM7016811,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 2,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016811,GSM7016811: zfCM 7dpi 2; Danio rerio; RNA Seq,GSM7016811 r1,GSM7016811,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-DB-005_HNWVVBGX9_S4_L001_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L001_R2_001.fastq.gz,fastq fastq,806178534.0,9374169.0,GSM7016811 r1,0:26 1:60,A:213590554;C:148614157;G:163804315;T:279996916;N:172592,26,60,,,213590554,148614157,163804315,279996916,172592,SRX19234271,SRS16638729,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10778,0.79221,0.1011,0.39378,0.99299,0.93695,0.65894,0.39542,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73968,SRR23291011,SRX19234271,SRS16638729,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 2,GSM7016811,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 2,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016811,GSM7016811: zfCM 7dpi 2; Danio rerio; RNA Seq,GSM7016811 r1,GSM7016811,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-DB-005_HNWVVBGX9_S4_L002_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L002_R2_001.fastq.gz,fastq fastq,874594286.0,10169701.0,GSM7016811 r2,0:26 1:60,A:227213153;C:160851586;G:182364146;T:303951184;N:214217,26,60,,,227213153,160851586,182364146,303951184,214217,SRX19234271,SRS16638729,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11066,0.80318,0.10409,0.40131,0.99289,0.9333,0.66859,0.40896,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73969,SRR23291012,SRX19234271,SRS16638729,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 2,GSM7016811,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 2,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016811,GSM7016811: zfCM 7dpi 2; Danio rerio; RNA Seq,GSM7016811 r1,GSM7016811,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-DB-005_HNWVVBGX9_S4_L003_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L003_R2_001.fastq.gz,fastq fastq,831835860.0,9672510.0,GSM7016811 r3,0:26 1:60,A:220300204;C:153061412;G:168938657;T:289375449;N:160138,26,60,,,220300204,153061412,168938657,289375449,160138,SRX19234271,SRS16638729,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10977,0.78663,0.1033,0.39172,0.99297,0.93669,0.64493,0.36881,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73970,SRR23291013,SRX19234271,SRS16638729,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 2,GSM7016811,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 2,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016811,GSM7016811: zfCM 7dpi 2; Danio rerio; RNA Seq,GSM7016811 r1,GSM7016811,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-DB-005_HNWVVBGX9_S4_L004_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L004_R2_001.fastq.gz,fastq fastq,692573136.0,8053176.0,GSM7016811 r4,0:26 1:60,A:182418113;C:126757471;G:143869511;T:239393143;N:134898,26,60,,,182418113,126757471,143869511,239393143,134898,SRX19234271,SRS16638729,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10826,0.81364,0.10182,0.40464,0.9931,0.94034,0.66059,0.40686,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73971,SRR23291015,SRX19234270,SRS16638728,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 1,GSM7016810,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 1,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016810,GSM7016810: zfCM 7dpi 1; Danio rerio; RNA Seq,GSM7016810 r1,GSM7016810,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-DB-001_AHVKTGBGX7_S5_L001_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L001_R2_001.fastq.gz,fastq fastq,471703034.0,5484919.0,GSM7016810 r1,0:26 1:60,A:125045012;C:89627491;G:85413855;T:171466861;N:149815,26,60,,,125045012,89627491,85413855,171466861,149815,SRX19234270,SRS16638728,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10906,0.67997,0.10214,0.30398,0.99117,0.94209,0.6357,0.45559,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73972,SRR23291016,SRX19234270,SRS16638728,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 1,GSM7016810,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 1,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016810,GSM7016810: zfCM 7dpi 1; Danio rerio; RNA Seq,GSM7016810 r1,GSM7016810,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-DB-001_AHVKTGBGX7_S5_L002_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L002_R2_001.fastq.gz,fastq fastq,489372938.0,5690383.0,GSM7016810 r2,0:26 1:60,A:131516821;C:92202683;G:88685608;T:176824985;N:142841,26,60,,,131516821,92202683,88685608,176824985,142841,SRX19234270,SRS16638728,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11042,0.68087,0.10314,0.3043,0.99145,0.94882,0.5723,0.46048,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73973,SRR23291017,SRX19234270,SRS16638728,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 1,GSM7016810,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 1,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016810,GSM7016810: zfCM 7dpi 1; Danio rerio; RNA Seq,GSM7016810 r1,GSM7016810,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-DB-001_AHVKTGBGX7_S5_L003_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L003_R2_001.fastq.gz,fastq fastq,407735288.0,4741108.0,GSM7016810 r3,0:26 1:60,A:108841476;C:77418215;G:73171345;T:148203998;N:100254,26,60,,,108841476,77418215,73171345,148203998,100254,SRX19234270,SRS16638728,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10889,0.67068,0.10168,0.29526,0.99117,0.9471,0.66379,0.42801,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73974,SRR23291018,SRX19234270,SRS16638728,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 1,GSM7016810,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 1,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016810,GSM7016810: zfCM 7dpi 1; Danio rerio; RNA Seq,GSM7016810 r1,GSM7016810,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-DB-001_AHVKTGBGX7_S5_L004_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L004_R2_001.fastq.gz,fastq fastq,505539304.0,5878364.0,GSM7016810 r4,0:26 1:60,A:135189083;C:94908231;G:92431583;T:182885125;N:125282,26,60,,,135189083,94908231,92431583,182885125,125282,SRX19234270,SRS16638728,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10989,0.68603,0.10295,0.30544,0.99119,0.94783,0.65617,0.41933,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
74146,SRR23570564,SRX19457378,SRS16850065,SRP423736,PRJNA937226,Single cell transcriptomics on zebrafish gliovascular niche,GSE225721,Transcriptome Analysis,To investigate the cell types involved in the gliovascular niche of the zebrafish brain  we performed single cell sequencing on cells sorted from fli1:gfp and her4: GFP transgenic animals in control and amyloid toxicity conditions.  Overall design: Tgher4.1:dRED and Tgfli1a:GFP lines were injected with Amyloid beta 42 peptide as descibed Bhatatrai et al. 2016 and cells were dissociated sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation  cDNA synthesis by 10X Genomics. The reads were aligned to zebrafish genom GRChZ 11 and ensemble version 105 was used for gene annotation and assigning reads to genes. Genomics Kit  and Sequencing done by Illumina.,,pubmed:38260431;pubmed:38598053;pubmed:38902234,,vascular  AB42,GSM7054715,,source name:telencephalon|tissue:telencephalon|genotype:Tgher4.1:dRED|treatment:AB42|geo loc name:missing|collection date:missing,vascular  AB42,The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genmoics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger,telencephalon,Tgher4.1:dRED and Tgfli1a:GFP lines were injected with Amyloid beta 42 peptide and PBS as control as descibed Bhatatrai et al. 2016.,Cells from zebrafish telencephalon were dissociated  cells were sorted by FACS based on the reporter line. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH 7.5  at 28 °C ±1 °C in groups of 20 animals per 2.8 L. ,tissue:telencephalon|genotype:Tgher4.1:dRED|treatment:AB42,GSM7054715,GSM7054715: vascular  AB42; Danio rerio; RNA Seq,GSM7054715 r1,GSM7054715,1,Cells from zebrafish telencephalon were dissociated  cells were sorted by FACS based on the reporter line. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP423736,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=CP016 S1 L003 I1 001.fastq.gz   read2PairFiles=CP016 S1 L003 I2 001.fastq.gz   read3PairFiles=CP016 S1 L003 R1 001.fastq.gz   read4PairFiles=CP016 S1 L003 R2 001.fastq.gz,CP016_S1_L003_I1_001.fastq.gz CP016_S1_L003_I2_001.fastq.gz CP016_S1_L003_R1_001.fastq.gz CP016_S1_L003_R2_001.fastq.gz,fastq fastq fastq fastq,45647403792.0,205618936.0,GSM7054715 r1,0:10 1:10 2:101 3:101,A:11366470668;C:7429340348;G:7578573984;T:15159480677;N:1159395,10,10,101,101,11366470668,7429340348,7578573984,15159480677,1159395,SRX19457378,SRS16850065,SRA1593841,Columbia University Irving Medical Center,Columbia University Irving Medical Center,2,0.00022,0.89681,4e-05,0.2846,0.99991,0.74371,0.5,0.53723,101,101,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-02-21,Undetermined,Undetermined,Brain,Nervous System
74147,SRR23570565,SRX19457378,SRS16850065,SRP423736,PRJNA937226,Single cell transcriptomics on zebrafish gliovascular niche,GSE225721,Transcriptome Analysis,To investigate the cell types involved in the gliovascular niche of the zebrafish brain  we performed single cell sequencing on cells sorted from fli1:gfp and her4: GFP transgenic animals in control and amyloid toxicity conditions.  Overall design: Tgher4.1:dRED and Tgfli1a:GFP lines were injected with Amyloid beta 42 peptide as descibed Bhatatrai et al. 2016 and cells were dissociated sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation  cDNA synthesis by 10X Genomics. The reads were aligned to zebrafish genom GRChZ 11 and ensemble version 105 was used for gene annotation and assigning reads to genes. Genomics Kit  and Sequencing done by Illumina.,,pubmed:38260431;pubmed:38598053;pubmed:38902234,,vascular  AB42,GSM7054715,,source name:telencephalon|tissue:telencephalon|genotype:Tgher4.1:dRED|treatment:AB42|geo loc name:missing|collection date:missing,vascular  AB42,The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genmoics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger,telencephalon,Tgher4.1:dRED and Tgfli1a:GFP lines were injected with Amyloid beta 42 peptide and PBS as control as descibed Bhatatrai et al. 2016.,Cells from zebrafish telencephalon were dissociated  cells were sorted by FACS based on the reporter line. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH 7.5  at 28 °C ±1 °C in groups of 20 animals per 2.8 L. ,tissue:telencephalon|genotype:Tgher4.1:dRED|treatment:AB42,GSM7054715,GSM7054715: vascular  AB42; Danio rerio; RNA Seq,GSM7054715 r1,GSM7054715,1,Cells from zebrafish telencephalon were dissociated  cells were sorted by FACS based on the reporter line. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP423736,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=CP016 S1 L004 I1 001.fastq.gz   read2PairFiles=CP016 S1 L004 I2 001.fastq.gz   read3PairFiles=CP016 S1 L004 R1 001.fastq.gz   read4PairFiles=CP016 S1 L004 R2 001.fastq.gz,CP016_S1_L004_I1_001.fastq.gz CP016_S1_L004_I2_001.fastq.gz CP016_S1_L004_R1_001.fastq.gz CP016_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,45689271216.0,205807528.0,GSM7054715 r2,0:10 1:10 2:101 3:101,A:11389510151;C:7463425109;G:7607679289;T:15111473568;N:1032539,10,10,101,101,11389510151,7463425109,7607679289,15111473568,1032539,SRX19457378,SRS16850065,SRA1593841,Columbia University Irving Medical Center,Columbia University Irving Medical Center,2,0.00031,0.89955,0.0001,0.28522,0.99991,0.74205,1.0,0.53119,101,101,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-02-21,Undetermined,Undetermined,Brain,Nervous System
74148,SRR23570566,SRX19457377,SRS16850064,SRP423736,PRJNA937226,Single cell transcriptomics on zebrafish gliovascular niche,GSE225721,Transcriptome Analysis,To investigate the cell types involved in the gliovascular niche of the zebrafish brain  we performed single cell sequencing on cells sorted from fli1:gfp and her4: GFP transgenic animals in control and amyloid toxicity conditions.  Overall design: Tgher4.1:dRED and Tgfli1a:GFP lines were injected with Amyloid beta 42 peptide as descibed Bhatatrai et al. 2016 and cells were dissociated sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation  cDNA synthesis by 10X Genomics. The reads were aligned to zebrafish genom GRChZ 11 and ensemble version 105 was used for gene annotation and assigning reads to genes. Genomics Kit  and Sequencing done by Illumina.,,pubmed:38260431;pubmed:38598053;pubmed:38902234,,glia  AB42,GSM7054714,,source name:telencephalon|tissue:telencephalon|genotype:Tgfli1a:GFP|treatment:AB42|geo loc name:missing|collection date:missing,glia  AB42,The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genmoics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger,telencephalon,Tgher4.1:dRED and Tgfli1a:GFP lines were injected with Amyloid beta 42 peptide and PBS as control as descibed Bhatatrai et al. 2016.,Cells from zebrafish telencephalon were dissociated  cells were sorted by FACS based on the reporter line. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH 7.5  at 28 °C ±1 °C in groups of 20 animals per 2.8 L. ,tissue:telencephalon|genotype:Tgfli1a:GFP|treatment:AB42,GSM7054714,GSM7054714: glia  AB42; Danio rerio; RNA Seq,GSM7054714 r1,GSM7054714,1,Cells from zebrafish telencephalon were dissociated  cells were sorted by FACS based on the reporter line. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP423736,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=CP015 S1 L003 I1 001.fastq.gz   read2PairFiles=CP015 S1 L003 I2 001.fastq.gz   read3PairFiles=CP015 S1 L003 R1 001.fastq.gz   read4PairFiles=CP015 S1 L003 R2 001.fastq.gz,CP015_S1_L003_I1_001.fastq.gz CP015_S1_L003_I2_001.fastq.gz CP015_S1_L003_R1_001.fastq.gz CP015_S1_L003_R2_001.fastq.gz,fastq fastq fastq fastq,53835436896.0,242501968.0,GSM7054714 r1,0:10 1:10 2:101 3:101,A:13406693068;C:8900736266;G:9050160835;T:17626430375;N:1376992,10,10,101,101,13406693068,8900736266,9050160835,17626430375,1376992,SRX19457377,SRS16850064,SRA1593841,Columbia University Irving Medical Center,Columbia University Irving Medical Center,2,0.00057,0.90048,8e-05,0.29704,0.99979,0.74828,0.5,0.51547,101,101,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-02-21,Undetermined,Undetermined,Brain,Nervous System
74149,SRR23570567,SRX19457377,SRS16850064,SRP423736,PRJNA937226,Single cell transcriptomics on zebrafish gliovascular niche,GSE225721,Transcriptome Analysis,To investigate the cell types involved in the gliovascular niche of the zebrafish brain  we performed single cell sequencing on cells sorted from fli1:gfp and her4: GFP transgenic animals in control and amyloid toxicity conditions.  Overall design: Tgher4.1:dRED and Tgfli1a:GFP lines were injected with Amyloid beta 42 peptide as descibed Bhatatrai et al. 2016 and cells were dissociated sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation  cDNA synthesis by 10X Genomics. The reads were aligned to zebrafish genom GRChZ 11 and ensemble version 105 was used for gene annotation and assigning reads to genes. Genomics Kit  and Sequencing done by Illumina.,,pubmed:38260431;pubmed:38598053;pubmed:38902234,,glia  AB42,GSM7054714,,source name:telencephalon|tissue:telencephalon|genotype:Tgfli1a:GFP|treatment:AB42|geo loc name:missing|collection date:missing,glia  AB42,The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genmoics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger,telencephalon,Tgher4.1:dRED and Tgfli1a:GFP lines were injected with Amyloid beta 42 peptide and PBS as control as descibed Bhatatrai et al. 2016.,Cells from zebrafish telencephalon were dissociated  cells were sorted by FACS based on the reporter line. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH 7.5  at 28 °C ±1 °C in groups of 20 animals per 2.8 L. ,tissue:telencephalon|genotype:Tgfli1a:GFP|treatment:AB42,GSM7054714,GSM7054714: glia  AB42; Danio rerio; RNA Seq,GSM7054714 r1,GSM7054714,1,Cells from zebrafish telencephalon were dissociated  cells were sorted by FACS based on the reporter line. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP423736,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=CP015 S1 L004 I1 001.fastq.gz   read2PairFiles=CP015 S1 L004 I2 001.fastq.gz   read3PairFiles=CP015 S1 L004 R1 001.fastq.gz   read4PairFiles=CP015 S1 L004 R2 001.fastq.gz,CP015_S1_L004_I1_001.fastq.gz CP015_S1_L004_I2_001.fastq.gz CP015_S1_L004_R1_001.fastq.gz CP015_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,53827244208.0,242465064.0,GSM7054714 r2,0:10 1:10 2:101 3:101,A:13421170280;C:8931159403;G:9070720063;T:17553668084;N:1225098,10,10,101,101,13421170280,8931159403,9070720063,17553668084,1225098,SRX19457377,SRS16850064,SRA1593841,Columbia University Irving Medical Center,Columbia University Irving Medical Center,2,0.00059,0.90392,0.00032,0.29777,0.99989,0.74988,1.0,0.51551,101,101,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-02-21,Undetermined,Undetermined,Brain,Nervous System
74150,SRR23570568,SRX19457376,SRS16850063,SRP423736,PRJNA937226,Single cell transcriptomics on zebrafish gliovascular niche,GSE225721,Transcriptome Analysis,To investigate the cell types involved in the gliovascular niche of the zebrafish brain  we performed single cell sequencing on cells sorted from fli1:gfp and her4: GFP transgenic animals in control and amyloid toxicity conditions.  Overall design: Tgher4.1:dRED and Tgfli1a:GFP lines were injected with Amyloid beta 42 peptide as descibed Bhatatrai et al. 2016 and cells were dissociated sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation  cDNA synthesis by 10X Genomics. The reads were aligned to zebrafish genom GRChZ 11 and ensemble version 105 was used for gene annotation and assigning reads to genes. Genomics Kit  and Sequencing done by Illumina.,,pubmed:38260431;pubmed:38598053;pubmed:38902234,,vascular  PBS,GSM7054713,,source name:telencephalon|tissue:telencephalon|genotype:Tgher4.1:dRED|treatment:PBS|geo loc name:missing|collection date:missing,vascular  PBS,The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genmoics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger,telencephalon,Tgher4.1:dRED and Tgfli1a:GFP lines were injected with Amyloid beta 42 peptide and PBS as control as descibed Bhatatrai et al. 2016.,Cells from zebrafish telencephalon were dissociated  cells were sorted by FACS based on the reporter line. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH 7.5  at 28 °C ±1 °C in groups of 20 animals per 2.8 L. ,tissue:telencephalon|genotype:Tgher4.1:dRED|treatment:PBS,GSM7054713,GSM7054713: vascular  PBS; Danio rerio; RNA Seq,GSM7054713 r1,GSM7054713,1,Cells from zebrafish telencephalon were dissociated  cells were sorted by FACS based on the reporter line. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP423736,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=CP014 S1 L003 I1 001.fastq.gz   read2PairFiles=CP014 S1 L003 I2 001.fastq.gz   read3PairFiles=CP014 S1 L003 R1 001.fastq.gz   read4PairFiles=CP014 S1 L003 R2 001.fastq.gz,CP014_S1_L003_I1_001.fastq.gz CP014_S1_L003_I2_001.fastq.gz CP014_S1_L003_R1_001.fastq.gz CP014_S1_L003_R2_001.fastq.gz,fastq fastq fastq fastq,51738372060.0,233055730.0,GSM7054713 r1,0:10 1:10 2:101 3:101,A:12905633167;C:8331171365;G:8521460282;T:17317666998;N:1325648,10,10,101,101,12905633167,8331171365,8521460282,17317666998,1325648,SRX19457376,SRS16850063,SRA1593841,Columbia University Irving Medical Center,Columbia University Irving Medical Center,2,0.00038,0.89145,0.00024,0.28233,0.99993,0.74535,0.66666,0.53557,101,101,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-02-21,Undetermined,Undetermined,Brain,Nervous System