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
56706,SRR11040640,SRX7692417,SRS6118510,SRP247644,PRJNA605419,FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development,GSE144944,Transcriptome Analysis,In order to study FGFRthree primes role in cranial vault development  we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton  with a lack of sutures  abnormal frontal and parietal bones  and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype  we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication  mineralization  and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377  we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells  chondrogenic cells  immune cells epidermal cells  endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,pubmed:32379366,,2 fgfr3lof/lof,GSM4301251,,source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm,2 fgfr3lof/lof,Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500  or ii more than 20% of mitochondrial counts. post data filtering  we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx,Cranial vault,,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer’s instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm,GSM4301251,GSM4301251: 2 fgfr3lof/lof; Danio rerio; RNA Seq,GSM4301251,,1,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer's instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,GEO Accession:GSM4301251,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP247644,,,2-fgfr3lof-R3-ZF-0519_S3_L001_R1_001.fastq.gz 2-fgfr3lof-R3-ZF-0519_S3_L001_R2_001.fastq.gz,fastq fastq,2956636039.0,24845681.0,GSM4301251 r1,0:28 1:91,A:805752236;C:683372886;G:699894274;T:767405768;N:210875,28,91,,,805752236,683372886,699894274,767405768,210875,SRX7692417,SRS6118510,SRA1039424,GEO,"Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine",2,0.00944,0.95293,0.0032,0.11845,0.98863,0.79573,0.31275,0.48226,28,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,10x,,France,2020-02-07,Undetermined,Undetermined,Multi-tissue,Multi-system
56707,SRR11040641,SRX7692417,SRS6118510,SRP247644,PRJNA605419,FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development,GSE144944,Transcriptome Analysis,In order to study FGFRthree primes role in cranial vault development  we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton  with a lack of sutures  abnormal frontal and parietal bones  and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype  we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication  mineralization  and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377  we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells  chondrogenic cells  immune cells epidermal cells  endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,pubmed:32379366,,2 fgfr3lof/lof,GSM4301251,,source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm,2 fgfr3lof/lof,Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500  or ii more than 20% of mitochondrial counts. post data filtering  we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx,Cranial vault,,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer’s instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm,GSM4301251,GSM4301251: 2 fgfr3lof/lof; Danio rerio; RNA Seq,GSM4301251,,1,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer's instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,GEO Accession:GSM4301251,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP247644,,,2-fgfr3lof-R3-ZF-0519_S4_L001_R1_001.fastq.gz 2-fgfr3lof-R3-ZF-0519_S4_L001_R2_001.fastq.gz,fastq fastq,2943149888.0,24732352.0,GSM4301251 r2,0:28 1:91,A:801299410;C:680335967;G:696876648;T:764428085;N:209778,28,91,,,801299410,680335967,696876648,764428085,209778,SRX7692417,SRS6118510,SRA1039424,GEO,"Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine",2,0.00982,0.95341,0.00295,0.11853,0.98798,0.79429,0.32383,0.48491,28,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,10x,,France,2020-02-07,Undetermined,Undetermined,Multi-tissue,Multi-system
56708,SRR11040642,SRX7692417,SRS6118510,SRP247644,PRJNA605419,FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development,GSE144944,Transcriptome Analysis,In order to study FGFRthree primes role in cranial vault development  we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton  with a lack of sutures  abnormal frontal and parietal bones  and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype  we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication  mineralization  and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377  we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells  chondrogenic cells  immune cells epidermal cells  endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,pubmed:32379366,,2 fgfr3lof/lof,GSM4301251,,source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm,2 fgfr3lof/lof,Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500  or ii more than 20% of mitochondrial counts. post data filtering  we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx,Cranial vault,,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer’s instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm,GSM4301251,GSM4301251: 2 fgfr3lof/lof; Danio rerio; RNA Seq,GSM4301251,,1,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer's instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,GEO Accession:GSM4301251,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP247644,,,2-fgfr3lof-R3-ZF-0519_S8_L001_R1_001.fastq.gz 2-fgfr3lof-R3-ZF-0519_S8_L001_R2_001.fastq.gz,fastq fastq,2930322283.0,24624557.0,GSM4301251 r3,0:28 1:91,A:800017449;C:676370110;G:692286275;T:761438555;N:209894,28,91,,,800017449,676370110,692286275,761438555,209894,SRX7692417,SRS6118510,SRA1039424,GEO,"Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine",2,0.0091,0.95344,0.00277,0.11835,0.98863,0.79523,0.30888,0.47399,28,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,10x,,France,2020-02-07,Undetermined,Undetermined,Multi-tissue,Multi-system
56709,SRR11040643,SRX7692417,SRS6118510,SRP247644,PRJNA605419,FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development,GSE144944,Transcriptome Analysis,In order to study FGFRthree primes role in cranial vault development  we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton  with a lack of sutures  abnormal frontal and parietal bones  and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype  we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication  mineralization  and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377  we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells  chondrogenic cells  immune cells epidermal cells  endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,pubmed:32379366,,2 fgfr3lof/lof,GSM4301251,,source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm,2 fgfr3lof/lof,Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500  or ii more than 20% of mitochondrial counts. post data filtering  we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx,Cranial vault,,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer’s instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm,GSM4301251,GSM4301251: 2 fgfr3lof/lof; Danio rerio; RNA Seq,GSM4301251,,1,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer's instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,GEO Accession:GSM4301251,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP247644,,,2-fgfr3lof-R3-ZF-0519_S10_L001_R1_001.fastq.gz 2-fgfr3lof-R3-ZF-0519_S10_L001_R2_001.fastq.gz,fastq fastq,3086393758.0,25936082.0,GSM4301251 r4,0:28 1:91,A:842498816;C:712567363;G:729291108;T:801817022;N:219449,28,91,,,842498816,712567363,729291108,801817022,219449,SRX7692417,SRS6118510,SRA1039424,GEO,"Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine",2,0.00907,0.95227,0.00303,0.11898,0.98906,0.79555,0.32194,0.48998,28,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,10x,,France,2020-02-07,Undetermined,Undetermined,Multi-tissue,Multi-system
56710,SRR11040636,SRX7692416,SRS6118508,SRP247644,PRJNA605419,FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development,GSE144944,Transcriptome Analysis,In order to study FGFRthree primes role in cranial vault development  we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton  with a lack of sutures  abnormal frontal and parietal bones  and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype  we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication  mineralization  and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377  we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells  chondrogenic cells  immune cells epidermal cells  endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,pubmed:32379366,,1 fgfr3lof/lof,GSM4301250,,source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm,1 fgfr3lof/lof,Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500  or ii more than 20% of mitochondrial counts. post data filtering  we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx,Cranial vault,,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer’s instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm,GSM4301250,GSM4301250: 1 fgfr3lof/lof; Danio rerio; RNA Seq,GSM4301250,,1,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer's instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,GEO Accession:GSM4301250,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP247644,,,1-fgfr3lof-R3-ZF-0519_S2_L001_R1_001.fastq.gz 1-fgfr3lof-R3-ZF-0519_S2_L001_R2_001.fastq.gz,fastq fastq,3809919113.0,32016127.0,GSM4301250 r1,0:28 1:91,A:1051323356;C:870053361;G:886403932;T:1001865374;N:273090,28,91,,,1051323356,870053361,886403932,1001865374,273090,SRX7692416,SRS6118508,SRA1039424,GEO,"Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine",2,0.0073,0.95159,0.00239,0.13839,0.98979,0.78293,0.32315,0.49047,28,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,10x,,France,2020-02-07,Undetermined,Undetermined,Multi-tissue,Multi-system
56711,SRR11040637,SRX7692416,SRS6118508,SRP247644,PRJNA605419,FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development,GSE144944,Transcriptome Analysis,In order to study FGFRthree primes role in cranial vault development  we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton  with a lack of sutures  abnormal frontal and parietal bones  and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype  we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication  mineralization  and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377  we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells  chondrogenic cells  immune cells epidermal cells  endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,pubmed:32379366,,1 fgfr3lof/lof,GSM4301250,,source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm,1 fgfr3lof/lof,Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500  or ii more than 20% of mitochondrial counts. post data filtering  we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx,Cranial vault,,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer’s instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm,GSM4301250,GSM4301250: 1 fgfr3lof/lof; Danio rerio; RNA Seq,GSM4301250,,1,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer's instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,GEO Accession:GSM4301250,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP247644,,,1-fgfr3lof-R3-ZF-0519_S5_L001_R1_001.fastq.gz 1-fgfr3lof-R3-ZF-0519_S5_L001_R2_001.fastq.gz,fastq fastq,5231239643.0,43959997.0,GSM4301250 r2,0:28 1:91,A:1444902743;C:1193884261;G:1216010955;T:1376068197;N:373487,28,91,,,1444902743,1193884261,1216010955,1376068197,373487,SRX7692416,SRS6118508,SRA1039424,GEO,"Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine",2,0.00703,0.95125,0.00257,0.13933,0.99062,0.78417,0.33564,0.4777,28,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,10x,,France,2020-02-07,Undetermined,Undetermined,Multi-tissue,Multi-system
56712,SRR11040638,SRX7692416,SRS6118508,SRP247644,PRJNA605419,FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development,GSE144944,Transcriptome Analysis,In order to study FGFRthree primes role in cranial vault development  we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton  with a lack of sutures  abnormal frontal and parietal bones  and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype  we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication  mineralization  and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377  we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells  chondrogenic cells  immune cells epidermal cells  endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,pubmed:32379366,,1 fgfr3lof/lof,GSM4301250,,source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm,1 fgfr3lof/lof,Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500  or ii more than 20% of mitochondrial counts. post data filtering  we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx,Cranial vault,,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer’s instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm,GSM4301250,GSM4301250: 1 fgfr3lof/lof; Danio rerio; RNA Seq,GSM4301250,,1,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer's instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,GEO Accession:GSM4301250,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP247644,,,1-fgfr3lof-R3-ZF-0519_S14_L001_R1_001.fastq.gz 1-fgfr3lof-R3-ZF-0519_S14_L001_R2_001.fastq.gz,fastq fastq,6034697060.0,50711740.0,GSM4301250 r3,0:28 1:91,A:1667295741;C:1376061258;G:1401956669;T:1588951873;N:431519,28,91,,,1667295741,1376061258,1401956669,1588951873,431519,SRX7692416,SRS6118508,SRA1039424,GEO,"Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine",2,0.00707,0.94822,0.00239,0.13943,0.99038,0.78311,0.36655,0.47115,28,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,10x,,France,2020-02-07,Undetermined,Undetermined,Multi-tissue,Multi-system
56713,SRR11040639,SRX7692416,SRS6118508,SRP247644,PRJNA605419,FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development,GSE144944,Transcriptome Analysis,In order to study FGFRthree primes role in cranial vault development  we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton  with a lack of sutures  abnormal frontal and parietal bones  and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype  we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication  mineralization  and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377  we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells  chondrogenic cells  immune cells epidermal cells  endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,pubmed:32379366,,1 fgfr3lof/lof,GSM4301250,,source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm,1 fgfr3lof/lof,Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500  or ii more than 20% of mitochondrial counts. post data filtering  we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx,Cranial vault,,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer’s instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,tissue:Cranial vault|genotype/variation:fgfr3lof1/lof1|length:9 mm,GSM4301250,GSM4301250: 1 fgfr3lof/lof; Danio rerio; RNA Seq,GSM4301250,,1,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer's instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,GEO Accession:GSM4301250,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP247644,,,1-fgfr3lof-R3-ZF-0519_S15_L001_R1_001.fastq.gz 1-fgfr3lof-R3-ZF-0519_S15_L001_R2_001.fastq.gz,fastq fastq,5425038164.0,45588556.0,GSM4301250 r4,0:28 1:91,A:1498130539;C:1238395410;G:1261876829;T:1426249730;N:385656,28,91,,,1498130539,1238395410,1261876829,1426249730,385656,SRX7692416,SRS6118508,SRA1039424,GEO,"Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine",2,0.00733,0.94973,0.0026,0.13793,0.99068,0.78423,0.3337,0.48233,28,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,10x,,France,2020-02-07,Undetermined,Undetermined,Multi-tissue,Multi-system
56714,SRR11040632,SRX7692415,SRS6118509,SRP247644,PRJNA605419,FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development,GSE144944,Transcriptome Analysis,In order to study FGFRthree primes role in cranial vault development  we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton  with a lack of sutures  abnormal frontal and parietal bones  and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype  we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication  mineralization  and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377  we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells  chondrogenic cells  immune cells epidermal cells  endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,pubmed:32379366,,2 fgfr3+/+,GSM4301249,,source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm,2 fgfr3+/+,Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500  or ii more than 20% of mitochondrial counts. post data filtering  we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx,Cranial vault,,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer’s instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm,GSM4301249,GSM4301249: 2 fgfr3+/+; Danio rerio; RNA Seq,GSM4301249,,1,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer's instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,GEO Accession:GSM4301249,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP247644,,,2-fgfr3plus-R3-ZF-0519_S6_L001_R1_001.fastq.gz 2-fgfr3plus-R3-ZF-0519_S6_L001_R2_001.fastq.gz,fastq fastq,4962416501.0,41700979.0,GSM4301249 r1,0:28 1:91,A:1356709063;C:1139750321;G:1170875983;T:1294727572;N:353562,28,91,,,1356709063,1139750321,1170875983,1294727572,353562,SRX7692415,SRS6118509,SRA1039424,GEO,"Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine",2,0.00727,0.95235,0.00248,0.13046,0.98981,0.78054,0.33659,0.48621,28,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,10x,,France,2020-02-07,Undetermined,Undetermined,Multi-tissue,Multi-system
56715,SRR11040633,SRX7692415,SRS6118509,SRP247644,PRJNA605419,FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development,GSE144944,Transcriptome Analysis,In order to study FGFRthree primes role in cranial vault development  we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton  with a lack of sutures  abnormal frontal and parietal bones  and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype  we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication  mineralization  and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377  we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells  chondrogenic cells  immune cells epidermal cells  endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,pubmed:32379366,,2 fgfr3+/+,GSM4301249,,source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm,2 fgfr3+/+,Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500  or ii more than 20% of mitochondrial counts. post data filtering  we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx,Cranial vault,,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer’s instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm,GSM4301249,GSM4301249: 2 fgfr3+/+; Danio rerio; RNA Seq,GSM4301249,,1,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer's instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,GEO Accession:GSM4301249,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP247644,,,2-fgfr3plus-R3-ZF-0519_S12_L001_R1_001.fastq.gz 2-fgfr3plus-R3-ZF-0519_S12_L001_R2_001.fastq.gz,fastq fastq,6695697316.0,56266364.0,GSM4301249 r2,0:28 1:91,A:1829441811;C:1538021924;G:1580312219;T:1747444971;N:476391,28,91,,,1829441811,1538021924,1580312219,1747444971,476391,SRX7692415,SRS6118509,SRA1039424,GEO,"Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine",2,0.00744,0.95393,0.0026,0.13086,0.98969,0.78139,0.34081,0.50162,28,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,10x,,France,2020-02-07,Undetermined,Undetermined,Multi-tissue,Multi-system
56716,SRR11040634,SRX7692415,SRS6118509,SRP247644,PRJNA605419,FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development,GSE144944,Transcriptome Analysis,In order to study FGFRthree primes role in cranial vault development  we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton  with a lack of sutures  abnormal frontal and parietal bones  and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype  we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication  mineralization  and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377  we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells  chondrogenic cells  immune cells epidermal cells  endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,pubmed:32379366,,2 fgfr3+/+,GSM4301249,,source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm,2 fgfr3+/+,Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500  or ii more than 20% of mitochondrial counts. post data filtering  we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx,Cranial vault,,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer’s instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm,GSM4301249,GSM4301249: 2 fgfr3+/+; Danio rerio; RNA Seq,GSM4301249,,1,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer's instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,GEO Accession:GSM4301249,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP247644,,,2-fgfr3plus-R3-ZF-0519_S13_L001_R1_001.fastq.gz 2-fgfr3plus-R3-ZF-0519_S13_L001_R2_001.fastq.gz,fastq fastq,4853594809.0,40786511.0,GSM4301249 r3,0:28 1:91,A:1328029955;C:1113808349;G:1144735618;T:1266673333;N:347554,28,91,,,1328029955,1113808349,1144735618,1266673333,347554,SRX7692415,SRS6118509,SRA1039424,GEO,"Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine",2,0.00737,0.95245,0.00274,0.12891,0.99038,0.78228,0.3487,0.4977,28,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,10x,,France,2020-02-07,Undetermined,Undetermined,Multi-tissue,Multi-system
56717,SRR11040635,SRX7692415,SRS6118509,SRP247644,PRJNA605419,FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development,GSE144944,Transcriptome Analysis,In order to study FGFRthree primes role in cranial vault development  we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton  with a lack of sutures  abnormal frontal and parietal bones  and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype  we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication  mineralization  and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377  we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells  chondrogenic cells  immune cells epidermal cells  endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,pubmed:32379366,,2 fgfr3+/+,GSM4301249,,source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm,2 fgfr3+/+,Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500  or ii more than 20% of mitochondrial counts. post data filtering  we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx,Cranial vault,,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer’s instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm,GSM4301249,GSM4301249: 2 fgfr3+/+; Danio rerio; RNA Seq,GSM4301249,,1,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer's instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,GEO Accession:GSM4301249,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP247644,,,2-fgfr3plus-R3-ZF-0519_S16_L001_R1_001.fastq.gz 2-fgfr3plus-R3-ZF-0519_S16_L001_R2_001.fastq.gz,fastq fastq,6323597406.0,53139474.0,GSM4301249 r4,0:28 1:91,A:1727515649;C:1453521438;G:1493844843;T:1648265752;N:449724,28,91,,,1727515649,1453521438,1493844843,1648265752,449724,SRX7692415,SRS6118509,SRA1039424,GEO,"Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine",2,0.00737,0.95341,0.00266,0.12818,0.98934,0.78151,0.32417,0.4918,28,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,10x,,France,2020-02-07,Undetermined,Undetermined,Multi-tissue,Multi-system
56718,SRR11040628,SRX7692414,SRS6118507,SRP247644,PRJNA605419,FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development,GSE144944,Transcriptome Analysis,In order to study FGFRthree primes role in cranial vault development  we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton  with a lack of sutures  abnormal frontal and parietal bones  and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype  we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication  mineralization  and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377  we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells  chondrogenic cells  immune cells epidermal cells  endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,pubmed:32379366,,1 fgfr3+/+,GSM4301248,,source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm,1 fgfr3+/+,Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500  or ii more than 20% of mitochondrial counts. post data filtering  we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx,Cranial vault,,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer’s instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm,GSM4301248,GSM4301248: 1 fgfr3+/+; Danio rerio; RNA Seq,GSM4301248,,1,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer's instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,GEO Accession:GSM4301248,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP247644,,,1-fgfr3plus-R3-ZF-0519_S1_L001_R1_001.fastq.gz 1-fgfr3plus-R3-ZF-0519_S1_L001_R2_001.fastq.gz,fastq fastq,6286029939.0,52823781.0,GSM4301248 r1,0:28 1:91,A:1726222024;C:1448493933;G:1483478967;T:1627385939;N:449076,28,91,,,1726222024,1448493933,1483478967,1627385939,449076,SRX7692414,SRS6118507,SRA1039424,GEO,"Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine",2,0.00651,0.95215,0.0021,0.11197,0.99099,0.79914,0.32593,0.49237,28,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,10x,,France,2020-02-07,Undetermined,Undetermined,Multi-tissue,Multi-system
56719,SRR11040629,SRX7692414,SRS6118507,SRP247644,PRJNA605419,FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development,GSE144944,Transcriptome Analysis,In order to study FGFRthree primes role in cranial vault development  we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton  with a lack of sutures  abnormal frontal and parietal bones  and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype  we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication  mineralization  and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377  we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells  chondrogenic cells  immune cells epidermal cells  endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,pubmed:32379366,,1 fgfr3+/+,GSM4301248,,source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm,1 fgfr3+/+,Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500  or ii more than 20% of mitochondrial counts. post data filtering  we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx,Cranial vault,,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer’s instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm,GSM4301248,GSM4301248: 1 fgfr3+/+; Danio rerio; RNA Seq,GSM4301248,,1,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer's instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,GEO Accession:GSM4301248,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP247644,,,1-fgfr3plus-R3-ZF-0519_S7_L001_R1_001.fastq.gz 1-fgfr3plus-R3-ZF-0519_S7_L001_R2_001.fastq.gz,fastq fastq,5384386336.0,45246944.0,GSM4301248 r2,0:28 1:91,A:1482057664;C:1241359922;G:1266945881;T:1393638700;N:384169,28,91,,,1482057664,1241359922,1266945881,1393638700,384169,SRX7692414,SRS6118507,SRA1039424,GEO,"Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine",2,0.00644,0.9527,0.00205,0.11156,0.99111,0.80217,0.3568,0.48853,28,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,10x,,France,2020-02-07,Undetermined,Undetermined,Multi-tissue,Multi-system
56720,SRR11040630,SRX7692414,SRS6118507,SRP247644,PRJNA605419,FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development,GSE144944,Transcriptome Analysis,In order to study FGFRthree primes role in cranial vault development  we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton  with a lack of sutures  abnormal frontal and parietal bones  and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype  we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication  mineralization  and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377  we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells  chondrogenic cells  immune cells epidermal cells  endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,pubmed:32379366,,1 fgfr3+/+,GSM4301248,,source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm,1 fgfr3+/+,Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500  or ii more than 20% of mitochondrial counts. post data filtering  we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx,Cranial vault,,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer’s instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm,GSM4301248,GSM4301248: 1 fgfr3+/+; Danio rerio; RNA Seq,GSM4301248,,1,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer's instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,GEO Accession:GSM4301248,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP247644,,,1-fgfr3plus-R3-ZF-0519_S9_L001_R1_001.fastq.gz 1-fgfr3plus-R3-ZF-0519_S9_L001_R2_001.fastq.gz,fastq fastq,5916050133.0,49714707.0,GSM4301248 r3,0:28 1:91,A:1628484212;C:1362413135;G:1391038139;T:1533691145;N:423502,28,91,,,1628484212,1362413135,1391038139,1533691145,423502,SRX7692414,SRS6118507,SRA1039424,GEO,"Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine",2,0.0066,0.95312,0.00209,0.11367,0.99109,0.79857,0.336,0.47399,28,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,10x,,France,2020-02-07,Undetermined,Undetermined,Multi-tissue,Multi-system
56721,SRR11040631,SRX7692414,SRS6118507,SRP247644,PRJNA605419,FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development,GSE144944,Transcriptome Analysis,In order to study FGFRthree primes role in cranial vault development  we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton  with a lack of sutures  abnormal frontal and parietal bones  and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype  we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication  mineralization  and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377  we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells  chondrogenic cells  immune cells epidermal cells  endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,pubmed:32379366,,1 fgfr3+/+,GSM4301248,,source name:Cranial vault|tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm,1 fgfr3+/+,Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500  or ii more than 20% of mitochondrial counts. post data filtering  we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx,Cranial vault,,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer’s instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,,tissue:Cranial vault|genotype/variation:fgfr3+/+|length:9 mm,GSM4301248,GSM4301248: 1 fgfr3+/+; Danio rerio; RNA Seq,GSM4301248,,1,The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs  the anterior parts of the frontal bones  and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS  cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer  and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry  the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells  beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics  according to the manufacturer's instructions. Briefly  cells were counted  diluted at 1000 cells/µL in PBS+0.04% BSA  and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription  the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation  end repair and A tailing  sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp  with a mean read depth of 25000 reads per cell.,GEO Accession:GSM4301248,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP247644,,,1-fgfr3plus-R3-ZF-0519_S11_L001_R1_001.fastq.gz 1-fgfr3plus-R3-ZF-0519_S11_L001_R2_001.fastq.gz,fastq fastq,5591429319.0,46986801.0,GSM4301248 r4,0:28 1:91,A:1539075154;C:1286758672;G:1316467634;T:1448729317;N:398542,28,91,,,1539075154,1286758672,1316467634,1448729317,398542,SRX7692414,SRS6118507,SRA1039424,GEO,"Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine",2,0.00664,0.95136,0.00216,0.11396,0.99131,0.8003,0.32678,0.49629,28,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,10x,,France,2020-02-07,Undetermined,Undetermined,Multi-tissue,Multi-system
63234,SRR18508141,SRX14639419,SRS12405515,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Preleukemic stage  Ick:IRF4 fish 5,GSM5976296,,tissue:Zebrafish|cells:mCherry sorted cells|transgenic:IRF4 overexpression,Preleukemic stage  Ick:IRF4 fish 5,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Assembly: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  The cells were harvested at different stages and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,cells:mCherry sorted cells|transgenic:IRF4 overexpression,GSM5976296,GSM5976296: Preleukemic stage  Ick:IRF4 fish 5; Danio rerio; RNA Seq,GSM5976296,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis.,GEO Accession:GSM5976296,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP305927,,loader:fastq load.py|options:  readTypes=TTB   read1PairFiles=22 PS5 I1.fastq.gz   read2PairFiles=22 PS5 R1.fastq.gz   read3PairFiles=22 PS5 R2.fastq.gz,22_PS5_I1.fastq.gz 22_PS5_R1.fastq.gz 22_PS5_R2.fastq.gz,fastq fastq fastq,29499386664.0,223480202.0,GSM5976296 r1,0:8 1:26 2:98,A:5916946346;C:5161367423;G:5141267981;T:5676847603;N:4630443,8,26,98,,5916946346,5161367423,5141267981,5676847603,4630443,SRX14639419,SRS12405515,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.80645,,0.12105,,0.84185,,0.60542,,98,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2022-03-28,Undetermined,Undetermined,Undetermined,Undetermined
63235,SRR18508140,SRX14639418,SRS12405514,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Preleukemic stage  Ick:IRF4 fish 4,GSM5976295,,tissue:Zebrafish|cells:mCherry sorted cells|transgenic:IRF4 overexpression,Preleukemic stage  Ick:IRF4 fish 4,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Assembly: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  The cells were harvested at different stages and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,cells:mCherry sorted cells|transgenic:IRF4 overexpression,GSM5976295,GSM5976295: Preleukemic stage  Ick:IRF4 fish 4; Danio rerio; RNA Seq,GSM5976295,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis.,GEO Accession:GSM5976295,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP305927,,loader:fastq load.py|options:  readTypes=TTB   read1PairFiles=21 PS4 I1.fastq.gz   read2PairFiles=21 PS4 R1.fastq.gz   read3PairFiles=21 PS4 R2.fastq.gz,21_PS4_I1.fastq.gz 21_PS4_R1.fastq.gz 21_PS4_R2.fastq.gz,fastq fastq fastq,27210025260.0,206136555.0,GSM5976295 r1,0:8 1:26 2:98,A:6014697783;C:4212623706;G:4664602896;T:5305183874;N:4274131,8,26,98,,6014697783,4212623706,4664602896,5305183874,4274131,SRX14639418,SRS12405514,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.90833,,0.21102,,0.81292,,0.52636,,98,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2022-03-28,Undetermined,Undetermined,Undetermined,Undetermined
63236,SRR18508139,SRX14639417,SRS12405513,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Preleukemic stage  Ick:IRF4 fish 3,GSM5976294,,tissue:Zebrafish|cells:mCherry sorted cells|transgenic:IRF4 overexpression,Preleukemic stage  Ick:IRF4 fish 3,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Assembly: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  The cells were harvested at different stages and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,cells:mCherry sorted cells|transgenic:IRF4 overexpression,GSM5976294,GSM5976294: Preleukemic stage  Ick:IRF4 fish 3; Danio rerio; RNA Seq,GSM5976294,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis.,GEO Accession:GSM5976294,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP305927,,loader:fastq load.py|options:  readTypes=TTB   read1PairFiles=20 PS3 I1.fastq.gz   read2PairFiles=20 PS3 R1.fastq.gz   read3PairFiles=20 PS3 R2.fastq.gz,20_PS3_I1.fastq.gz 20_PS3_R1.fastq.gz 20_PS3_R2.fastq.gz,fastq fastq fastq,27905597412.0,211406041.0,GSM5976294 r1,0:8 1:26 2:98,A:5697185546;C:4728899722;G:4759285311;T:5528101272;N:4320167,8,26,98,,5697185546,4728899722,4759285311,5528101272,4320167,SRX14639417,SRS12405513,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.86766,,0.13828,,0.81099,,0.56202,,98,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2022-03-28,Undetermined,Undetermined,Undetermined,Undetermined
63237,SRR18508138,SRX14639416,SRS12405512,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Preleukemic stage  Ick:IRF4 fish 2,GSM5976293,,tissue:Zebrafish|cells:mCherry sorted cells|transgenic:IRF4 overexpression,Preleukemic stage  Ick:IRF4 fish 2,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Assembly: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  The cells were harvested at different stages and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,cells:mCherry sorted cells|transgenic:IRF4 overexpression,GSM5976293,GSM5976293: Preleukemic stage  Ick:IRF4 fish 2; Danio rerio; RNA Seq,GSM5976293,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis.,GEO Accession:GSM5976293,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP305927,,loader:fastq load.py|options:  readTypes=TTB   read1PairFiles=19 PS2 I1.fastq.gz   read2PairFiles=19 PS2 R1.fastq.gz   read3PairFiles=19 PS2 R2.fastq.gz,19_PS2_I1.fastq.gz 19_PS2_R1.fastq.gz 19_PS2_R2.fastq.gz,fastq fastq fastq,24632876400.0,186612700.0,GSM5976293 r1,0:8 1:26 2:98,A:4778279544;C:4417666940;G:4309561799;T:4778714812;N:3821505,8,26,98,,4778279544,4417666940,4309561799,4778714812,3821505,SRX14639416,SRS12405512,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.8543,,0.09898,,0.8521,,0.57296,,98,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2022-03-28,Undetermined,Undetermined,Undetermined,Undetermined
63238,SRR18508137,SRX14639415,SRS12405511,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Preleukemic stage  Ick:IRF4 fish 1,GSM5976292,,tissue:Zebrafish|cells:mCherry sorted cells|transgenic:IRF4 overexpression,Preleukemic stage  Ick:IRF4 fish 1,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Assembly: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  The cells were harvested at different stages and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,cells:mCherry sorted cells|transgenic:IRF4 overexpression,GSM5976292,GSM5976292: Preleukemic stage  Ick:IRF4 fish 1; Danio rerio; RNA Seq,GSM5976292,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis.,GEO Accession:GSM5976292,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP305927,,loader:fastq load.py|options:  readTypes=TTB   read1PairFiles=18 PS1 I1.fastq.gz   read2PairFiles=18 PS1 R1.fastq.gz   read3PairFiles=18 PS1 R2.fastq.gz,18_PS1_I1.fastq.gz 18_PS1_R1.fastq.gz 18_PS1_R2.fastq.gz,fastq fastq fastq,32112448896.0,243276128.0,GSM5976292 r1,0:8 1:26 2:98,A:7019250955;C:4996601756;G:5458243501;T:6361897622;N:5066710,8,26,98,,7019250955,4996601756,5458243501,6361897622,5066710,SRX14639415,SRS12405511,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.90268,,0.1795,,0.79371,,0.53243,,98,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2022-03-28,Undetermined,Undetermined,Undetermined,Undetermined
63239,SRR13693865,SRX10083163,SRS8241179,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells  Late stage  IRF4;p53+/  fish 5 scRNA Seq,GSM5076953,,source name:Zebrafish cells  transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage,Tumor cells  Late stage  IRF4;p53+/  fish 5 scRNA Seq,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish cells  transgenic,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage,GSM5076953,GSM5076953: Tumor cells  Late stage  IRF4;p53+/  fish 5 scRNA Seq; Danio rerio; RNA Seq,GSM5076953,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,GEO Accession:GSM5076953,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP305927,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=S3 I1.fastq.gz   read2PairFiles=S3 R1.fastq.gz   read3PairFiles=S3 R2.fastq.gz,,,30902398692.0,234109081.0,GSM5076953 r1,0:8 1:26 2:98,A:8591012397;C:7005723022;G:7425233397;T:7870465271;N:9964605,8,26,98,,8591012397,7005723022,7425233397,7870465271,9964605,SRX10083163,SRS8241179,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.92664,,0.18689,,0.83376,,0.51575,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2021-02-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
63240,SRR13693864,SRX10083162,SRS8241178,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells  Late stage  IRF4;p53+/  fish 4 scRNA Seq,GSM5076952,,source name:Zebrafish cells  transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage,Tumor cells  Late stage  IRF4;p53+/  fish 4 scRNA Seq,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish cells  transgenic,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage,GSM5076952,GSM5076952: Tumor cells  Late stage  IRF4;p53+/  fish 4 scRNA Seq; Danio rerio; RNA Seq,GSM5076952,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,GEO Accession:GSM5076952,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP305927,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=S2 I1.fastq.gz   read2PairFiles=S2 R1.fastq.gz   read3PairFiles=S2 R2.fastq.gz,S2_I1.fastq S2_R1.fastq S2_R2.fastq,fastq fastq fastq,31435037700.0,238144225.0,GSM5076952 r1,0:8 1:26 2:98,A:8766861031;C:6971129836;G:7458655794;T:8228099570;N:10291469,8,26,98,,8766861031,6971129836,7458655794,8228099570,10291469,SRX10083162,SRS8241178,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.92786,,0.2437,,0.82406,,0.51326,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2021-02-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
63241,SRR13693863,SRX10083161,SRS8241177,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells  Late stage  IRF4;p53+/  fish 3 scRNA Seq,GSM5076951,,source name:Zebrafish cells  transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage,Tumor cells  Late stage  IRF4;p53+/  fish 3 scRNA Seq,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish cells  transgenic,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage,GSM5076951,GSM5076951: Tumor cells  Late stage  IRF4;p53+/  fish 3 scRNA Seq; Danio rerio; RNA Seq,GSM5076951,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,GEO Accession:GSM5076951,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP305927,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=D3 I1.fastq.gz   read2PairFiles=D3 R1.fastq.gz   read3PairFiles=D3 R2.fastq.gz,D3_I1.fastq.gz D3_R1.fastq.gz D3_R2.fastq.gz,fastq fastq fastq,28995027468.0,219659299.0,GSM5076951 r1,0:8 1:26 2:98,A:8296536133;C:6414043957;G:6689913049;T:7585241915;N:9292414,8,26,98,,8296536133,6414043957,6689913049,7585241915,9292414,SRX10083161,SRS8241177,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.91752,,0.20118,,0.82903,,0.51629,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2021-02-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
63242,SRR13693862,SRX10083160,SRS8241176,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells  Late stage  IRF4;p53+/  fish 2 scRNA Seq,GSM5076950,,source name:Zebrafish cells  transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage,Tumor cells  Late stage  IRF4;p53+/  fish 2 scRNA Seq,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish cells  transgenic,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage,GSM5076950,GSM5076950: Tumor cells  Late stage  IRF4;p53+/  fish 2 scRNA Seq; Danio rerio; RNA Seq,GSM5076950,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,GEO Accession:GSM5076950,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP305927,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=D2 I1.fastq.gz   read2PairFiles=D2 R1.fastq.gz   read3PairFiles=D2 R2.fastq.gz,D2_I1.fastq.gz D2_R1.fastq.gz D2_R2.fastq.gz,fastq fastq fastq,34413827844.0,260710817.0,GSM5076950 r1,0:8 1:26 2:98,A:9806323881;C:7657614846;G:7929340289;T:9009399182;N:11149646,8,26,98,,9806323881,7657614846,7929340289,9009399182,11149646,SRX10083160,SRS8241176,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.91903,,0.19966,,0.83591,,0.53703,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2021-02-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
63243,SRR13693861,SRX10083159,SRS8241175,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells  Late stage  IRF4;p53+/  fish 1 scRNA Seq,GSM5076949,,source name:Zebrafish cells  transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage,Tumor cells  Late stage  IRF4;p53+/  fish 1 scRNA Seq,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish cells  transgenic,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage,GSM5076949,GSM5076949: Tumor cells  Late stage  IRF4;p53+/  fish 1 scRNA Seq; Danio rerio; RNA Seq,GSM5076949,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,GEO Accession:GSM5076949,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP305927,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=D1 I1.fastq.gz   read2PairFiles=D1 R1.fastq.gz   read3PairFiles=D1 R2.fastq.gz,D1_I1.fastq.gz D1_R1.fastq.gz D1_R2.fastq.gz,fastq fastq fastq,32611994976.0,247060568.0,GSM5076949 r1,0:8 1:26 2:98,A:9284005966;C:7280091614;G:7543060588;T:8494420994;N:10415814,8,26,98,,9284005966,7280091614,7543060588,8494420994,10415814,SRX10083159,SRS8241175,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.92638,,0.18797,,0.83713,,0.55228,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2021-02-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
63244,SRR13693860,SRX10083158,SRS8241174,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells  Late stage  Ick:IRF4 fish 6 scRNA Seq,GSM5076948,,source name:Zebrafish cells  transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage,Tumor cells  Late stage  Ick:IRF4 fish 6 scRNA Seq,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish cells  transgenic,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage,GSM5076948,GSM5076948: Tumor cells  Late stage  Ick:IRF4 fish 6 scRNA Seq; Danio rerio; RNA Seq,GSM5076948,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,GEO Accession:GSM5076948,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP305927,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=3S I1.fastq.gz   read2PairFiles=3S R1.fastq.gz   read3PairFiles=3S R2.fastq.gz,3S_I1.fastq.gz 3S_R1.fastq.gz 3S_R2.fastq.gz,fastq fastq fastq,27615581268.0,209208949.0,GSM5076948 r1,0:8 1:26 2:98,A:7903060121;C:6181635403;G:6459419292;T:7062664494;N:8801958,8,26,98,,7903060121,6181635403,6459419292,7062664494,8801958,SRX10083158,SRS8241174,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.91885,,0.167,,0.84952,,0.49561,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2021-02-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
63245,SRR13693859,SRX10083157,SRS8241173,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells  Late stage  Ick:IRF4 fish 5 scRNA Seq,GSM5076947,,source name:Zebrafish cells  transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage,Tumor cells  Late stage  Ick:IRF4 fish 5 scRNA Seq,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish cells  transgenic,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage,GSM5076947,GSM5076947: Tumor cells  Late stage  Ick:IRF4 fish 5 scRNA Seq; Danio rerio; RNA Seq,GSM5076947,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,GEO Accession:GSM5076947,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP305927,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=2S I1.fastq.gz   read2PairFiles=2S R1.fastq.gz   read3PairFiles=2S R2.fastq.gz,2S_I1.fastq.gz 2S_R1.fastq.gz 2S_R2.fastq.gz,fastq fastq fastq,27096206280.0,205274290.0,GSM5076947 r1,0:8 1:26 2:98,A:7673974628;C:6078379871;G:6323826541;T:7011380350;N:8644890,8,26,98,,7673974628,6078379871,6323826541,7011380350,8644890,SRX10083157,SRS8241173,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.92045,,0.17808,,0.83942,,0.50762,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2021-02-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
63246,SRR13693858,SRX10083156,SRS8241172,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells  Late stage  Ick:IRF4 fish 4 scRNA Seq,GSM5076946,,source name:Zebrafish cells  transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage,Tumor cells  Late stage  Ick:IRF4 fish 4 scRNA Seq,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish cells  transgenic,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage,GSM5076946,GSM5076946: Tumor cells  Late stage  Ick:IRF4 fish 4 scRNA Seq; Danio rerio; RNA Seq,GSM5076946,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,GEO Accession:GSM5076946,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP305927,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=1S I1.fastq.gz   read2PairFiles=1S R1.fastq.gz   read3PairFiles=1S R2.fastq.gz,1S_I1.fastq.gz 1S_R1.fastq.gz 1S_R2.fastq.gz,fastq fastq fastq,25321669296.0,191830828.0,GSM5076946 r1,0:8 1:26 2:98,A:7267370389;C:5631756169;G:5928757429;T:6485676974;N:8108335,8,26,98,,7267370389,5631756169,5928757429,6485676974,8108335,SRX10083156,SRS8241172,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.92297,,0.2138,,0.84218,,0.52396,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2021-02-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
63247,SRR13693857,SRX10083155,SRS8241171,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells  Late stage  Ick:IRF4 fish 3 scRNA Seq,GSM5076945,,source name:Zebrafish cells  transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage,Tumor cells  Late stage  Ick:IRF4 fish 3 scRNA Seq,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish cells  transgenic,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage,GSM5076945,GSM5076945: Tumor cells  Late stage  Ick:IRF4 fish 3 scRNA Seq; Danio rerio; RNA Seq,GSM5076945,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,GEO Accession:GSM5076945,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP305927,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=10G I1.fastq.gz   read2PairFiles=10G R1.fastq.gz   read3PairFiles=10G R2.fastq.gz,,,29362596648.0,222443914.0,GSM5076945 r1,0:8 1:26 2:98,A:8309910202;C:6578384206;G:7008276151;T:7440260771;N:25765318,8,26,98,,8309910202,6578384206,7008276151,7440260771,25765318,SRX10083155,SRS8241171,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.92108,,0.20892,,0.85484,,0.52156,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2021-02-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
63248,SRR13693856,SRX10083154,SRS8241170,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells  Late stage  Ick:IRF4 fish 2 scRNA Seq,GSM5076944,,source name:Zebrafish cells  transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage,Tumor cells  Late stage  Ick:IRF4 fish 2 scRNA Seq,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish cells  transgenic,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage,GSM5076944,GSM5076944: Tumor cells  Late stage  Ick:IRF4 fish 2 scRNA Seq; Danio rerio; RNA Seq,GSM5076944,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,GEO Accession:GSM5076944,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP305927,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=10F I1.fastq.gz   read2PairFiles=10F R1.fastq.gz   read3PairFiles=10F R2.fastq.gz,10F_I1.fastq.gz 10F_R1.fastq.gz 10F_R2.fastq.gz,fastq fastq fastq,30225931824.0,228984332.0,GSM5076944 r1,0:8 1:26 2:98,A:8484220529;C:6779948314;G:7231863744;T:7703283562;N:26615675,8,26,98,,8484220529,6779948314,7231863744,7703283562,26615675,SRX10083154,SRS8241170,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.92746,,0.1895,,0.85817,,0.49147,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2021-02-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
63249,SRR13693855,SRX10083153,SRS8241169,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells  Late stage  Ick:IRF4 fish 1 scRNA Seq,GSM5076943,,source name:Zebrafish cells  transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage,Tumor cells  Late stage  Ick:IRF4 fish 1 scRNA Seq,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish cells  transgenic,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage,GSM5076943,GSM5076943: Tumor cells  Late stage  Ick:IRF4 fish 1 scRNA Seq; Danio rerio; RNA Seq,GSM5076943,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,GEO Accession:GSM5076943,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP305927,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=10E I1.fastq.gz   read2PairFiles=10E R1.fastq.gz   read3PairFiles=10E R2.fastq.gz,10E_I1.fastq 10E_R1.fastq 10E_R2.fastq,fastq fastq fastq,34321213080.0,260009190.0,GSM5076943 r1,0:8 1:26 2:98,A:9548435346;C:7827936248;G:8159132985;T:8755456452;N:30252049,8,26,98,,9548435346,7827936248,8159132985,8755456452,30252049,SRX10083153,SRS8241169,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.92658,,0.1882,,0.84861,,0.50119,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2021-02-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
63250,SRR13693854,SRX10083152,SRS8241168,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells  Early stage  Ick:IRF4 fish 3 scRNA Seq,GSM5076942,,source name:Zebrafish cells  transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Early stage,Tumor cells  Early stage  Ick:IRF4 fish 3 scRNA Seq,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish cells  transgenic,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Early stage,GSM5076942,GSM5076942: Tumor cells  Early stage  Ick:IRF4 fish 3 scRNA Seq; Danio rerio; RNA Seq,GSM5076942,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,GEO Accession:GSM5076942,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP305927,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=3D I1.fastq.gz   read2PairFiles=3D R1.fastq.gz   read3PairFiles=3D R2.fastq.gz,3D_I1.fastq 3D_R1.fastq 3D_R2.fastq,fastq fastq fastq,29652167556.0,224637633.0,GSM5076942 r1,0:8 1:26 2:98,A:8364846981;C:6574443334;G:6910197942;T:7776537448;N:26141851,8,26,98,,8364846981,6574443334,6910197942,7776537448,26141851,SRX10083152,SRS8241168,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.91807,,0.19059,,0.83205,,0.56087,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2021-02-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
63251,SRR13693853,SRX10083151,SRS8241167,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells  Early stage  Ick:IRF4 fish 2 scRNA Seq,GSM5076941,,source name:Zebrafish cells  transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Early stage,Tumor cells  Early stage  Ick:IRF4 fish 2 scRNA Seq,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish cells  transgenic,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Early stage,GSM5076941,GSM5076941: Tumor cells  Early stage  Ick:IRF4 fish 2 scRNA Seq; Danio rerio; RNA Seq,GSM5076941,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,GEO Accession:GSM5076941,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP305927,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=3C I1.fastq.gz   read2PairFiles=3C R1.fastq.gz   read3PairFiles=3C R2.fastq.gz,3C_I1.fastq.gz 3C_R1.fastq.gz 3C_R2.fastq.gz,fastq fastq fastq,29997585156.0,227254433.0,GSM5076941 r1,0:8 1:26 2:98,A:8572344693;C:6580024899;G:7240023287;T:7578830064;N:26362213,8,26,98,,8572344693,6580024899,7240023287,7578830064,26362213,SRX10083151,SRS8241167,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.93097,,0.27389,,0.86318,,0.50798,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2021-02-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
63252,SRR13693852,SRX10083150,SRS8241166,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells  Early stage  Ick:IRF4 fish 1 scRNA Seq,GSM5076940,,source name:Zebrafish cells  transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Early stage,Tumor cells  Early stage  Ick:IRF4 fish 1 scRNA Seq,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish cells  transgenic,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Early stage,GSM5076940,GSM5076940: Tumor cells  Early stage  Ick:IRF4 fish 1 scRNA Seq; Danio rerio; RNA Seq,GSM5076940,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,GEO Accession:GSM5076940,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP305927,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=3A I1.fastq.gz   read2PairFiles=3A R1.fastq.gz   read3PairFiles=3A R2.fastq.gz,,,29170933836.0,220991923.0,GSM5076940 r1,0:8 1:26 2:98,A:8114837766;C:6514920127;G:6820788482;T:7694661638;N:25725823,8,26,98,,8114837766,6514920127,6820788482,7694661638,25725823,SRX10083150,SRS8241166,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.91826,,0.16532,,0.82755,,0.51956,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2021-02-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
63253,SRR13693851,SRX10083149,SRS8241165,SRP305927,PRJNA701473,Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors,GSE166646,Transcriptome Analysis,Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4.  Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter.  Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry.  Normal cells was prepared from a control zebrafish which overexpresses only mCherry.  Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.,parent bioproject:PRJNA701471,pubmed:35504924,,Normal cells  Control scRNA Seq,GSM5076939,,source name:Zebrafish cells  control|tissue:normal cells|sorted cells:mCherry sorted cells|genotype:Control,Normal cells  Control scRNA Seq,Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information.  Single cell data were generated using mkref from cellranger package. Alignment  barcode assignation  and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count   id zv11 {sampleID}   fastqs={directory scSeq}   sample={sampleID}  transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze,Zebrafish cells  control,No treatment,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.,tissue:normal cells|sorted cells:mCherry sorted cells|genotype:Control,GSM5076939,GSM5076939: Normal cells  Control scRNA Seq; Danio rerio; RNA Seq,GSM5076939,,1,post sorting  the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5  P7  Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally  each fragment contains the 10x Barcode  UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq,GEO Accession:GSM5076939,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP305927,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=PC8 I1.fastq.gz   read2PairFiles=PC8 R1.fastq.gz   read3PairFiles=PC8 R2.fastq.gz,PC8_I1.fastq.gz PC8_R1.fastq.gz PC8_R2.fastq.gz,fastq fastq fastq,27368502216.0,207337138.0,GSM5076939 r1,0:8 1:26 2:98,A:7549832339;C:6248269949;G:6287147333;T:7274505713;N:8746882,8,26,98,,7549832339,6248269949,6287147333,7274505713,8746882,SRX10083149,SRS8241165,SRA1195246,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.89463,,0.1714,,0.81093,,0.53939,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Singapore,2021-02-11,Undetermined,Undetermined,Multi-tissue,Multi-system
66718,SRR16490737,SRX12693840,SRS10644723,SRP342163,PRJNA772751,Single cell transcriptomic atlas reveals the evolution of immune cells and molecules across multiple vertebrate species,GSE186158,Other,We utilized single cell RNA sequencing scRNA seq to carry out comparative transcriptome analysis in various immune cells from the spleens across seven vertebrate species. Overall design: High dimensional single cell RNA sequencing 10X Genomics was used to profile the transcriptomes of total immune cells isolated from seven organism  spleens.,,pubmed:36871615,,Fish,GSM5639492,,tissue:Fish splenocytes|cell type:Splenocytes,Fish,The 10x Genomics Cell Ranger 3.0.1 version pipeline was used to demultiplex raw files into FASTQ files  extract barcodes and UMI  filter  and map reads to the corresponding reference genome  and generate a matrix containing UMI counts. A 10x Genomics Cell Ranger pipeline was used to identify clonotypes by alignment and annotation with the default settings. Genome build: Fish:GRCz11  Frog:Xenopus laevis v2  Mouse:GRCm38  Rat:Rnor 6.0  Pig:Sscrofa11  Monkey:Mmul 8  Human:GRCh38 Supplementary files format and content: Supplementary files format and content: filtered feature bc matrix.tar contains counts matrix stored in the Market Exchange Format for sparse matrices.,Fish splenocytes,Splenocytes were sorted from the spleens of  seven vertebrate species,Spleen tissues were processed with the flat end of a syringe in a 100 mm culture dish containing 5 ml cold FACS buffer 2% FBS in PBS  then passed through a 70 μm cell strainer into a 15 ml tube. Cells were centrifuged to remove the supernatant. Cell pellets were treated with 1ml ACK Ammonium Chloride Potassium Lysing Buffer to remove the red blood cells. post washing with 10 ml cold FACS buffer  the remaining cells were stained with 7AAD Part 76332; Lot B226294 Biolegend for 30 min at 4 °C  then washed and resuspended in cold FACS buffer for flow cytometric sorting using FACS Aria II Cell Sorter BD Biosciences. Sorted 7AAD  cells with a viability higher than 90% were used for 10X genomics scRNA seq. Finally  libraries were sequenced on a NovaSeq 6000 system with NovaSeq 6000 S4 Reagent Kit 300 cycles. RNA libraries were prepared for sequencing using standard Illumina protocols,,cell type:Splenocytes,GSM5639492,GSM5639492: Fish; Danio rerio; RNA Seq,GSM5639492 r1,GSM5639492,1,Spleen tissues were processed with the flat end of a syringe in a 100 mm culture dish containing 5 ml cold FACS buffer 2% FBS in PBS  then passed through a 70 μm cell strainer into a 15 ml tube. Cells were centrifuged to remove the supernatant. Cell pellets were treated with 1ml ACK Ammonium Chloride Potassium Lysing Buffer to remove the red blood cells. post washing with 10 ml cold FACS buffer  the remaining cells were stained with 7AAD Part 76332; Lot B226294 Biolegend for 30 min at 4 °C  then washed and resuspended in cold FACS buffer for flow cytometric sorting using FACS Aria II Cell Sorter BD Biosciences. Sorted 7AAD  cells with a viability higher than 90% were used for 10X genomics scRNA seq. Finally  libraries were sequenced on a NovaSeq 6000 system with NovaSeq 6000 S4 Reagent Kit 300 cycles. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342163,,,fish5_S1_L002_R1_001.fastq.gz fish5_S1_L002_R2_001.fastq.gz,fastq fastq,128052138306.0,424013703.0,GSM5639492 r1,0:151 1:151,A:31857061588;C:30793041207;G:30850699878;T:34545754656;N:5580977,151,151,,,31857061588,30793041207,30850699878,34545754656,5580977,SRX12693840,SRS10644723,SRA1377133,xian jiaotong university,xian jiaotong university,2,0.06618,0.94142,0.01504,0.09555,0.96631,0.81266,0.69482,0.58057,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-10-19,Undetermined,Undetermined,Multi-tissue,Multi-system
66803,SRR16646359,SRX12847065,SRS10790601,SRP343918,PRJNA776627,Enrichment and single cell sequencing of the ventricular cells from zebrafish telencephalon,GSE186874,Other,Zebfrafish brains were injected with neutral cell tracking dye. Zebrafish telencephalon were dissociated and dye postive cells were sorted by FACS and single cell sequencing performed from these cells. Overall design: Zebrafish ventricular cells fom telencephalon were enriched by using cell tracking dye  single cell sequencing of these cells was performed by  10X Genomics.,,pubmed:35681503,,AS2,GSM5662814,,tissue:telencephalon|tag:wilt type,AS2,The fastq files were aligned to zebrafish transcript Ensembl Version 95by 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. Genome build: danRer11 Supplementary files format and content: tab delimited file  with gene names in rows and cell names and counts in columns.,telencephalon,Zebfrafish brains were injected with neutral cell tracking dye and 5 6 min post injection fish were sacrificed.,Cells from telencephalon were dissociated and cell tracking dye positve cells were sorted.  The library preparation was performed by 10X Genomics as per manufactur protocol,Fish were kept at 28 °C water system with 14/10 hours light/dark cycles,tag:wilt type,GSM5662814,GSM5662814: AS2; Danio rerio; RNA Seq,GSM5662814,,1,Cells from telencephalon were dissociated and cell tracking dye positve cells were sorted.  The library preparation was performed by 10X Genomics as per manufactur protocol,GEO Accession:GSM5662814,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP343918,,assembly:danRer11|intentional duplicate,WTAB_12M_possorted_genome_bam.bam,10X Genomics bam file,9121417308.0,98079756.0,GSM5662814 r1,0:93,A:2807824317;C:1747195814;G:1887252370;T:2679004798;N:140009,93,,,,2807824317,1747195814,1887252370,2679004798,140009,SRX12847065,SRS10790601,SRA1320126,GEO,"AG KIZIL, German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association",1,0.88535,,0.29534,,0.73933,,0.50975,,93,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2021-10-31,Undetermined,Undetermined,Brain,Nervous System
67832,SRR17375072,SRX13549231,SRS11443005,SRP352824,PRJNA793009,Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches single cells,GSE192740,Other,Analysis of CITE seq data   Nuclei RNA seq data and single cell RNA seq data on CD45+ and CD45  cells isolated from the livers of mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar  from healthy and steatotic human livers  from hamster liver  pig liver  chicken liver  monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers  NAFLD mouse livers  healthy human livers and steatotic human livers. Overall design: Single cell RNA Seq = Liver CD45+ and CD45  cells derived from mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar. Liver CD45+ and CD45  cells derived from healthy and obese humans. 10 Visium Spatial Seq = mouse StSt liver  mouse StSt capsule  mouse NAFLD liver   human non steatotic liver  human steatotic liver,parent bioproject:PRJNA793005,pubmed:35021063;pubmed:36304458,,Zebrafish 002 Whole Liver Cells Zebrafish,GSM5764413,,tissue:Liver|shortfilename:CS131|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics – v3|digestion method:Ex Vivo|number of added abs:0|number of cells:1241,Zebrafish 002 Whole Liver Cells Zebrafish,Raw data bcl files were first demultiplexed using Cell Ranger mkfastq version 3.1.0 or version 3.0.2 Demultiplexed data was then processed using the Cell Ranger count pipeline version 3.1.0 or version 3.0.2. Cite seq samples were mapped against the TotalSeqA whitelist. Genome build: mm10 Mouse  hg19 Human  GRCz10 Zebrafish  MesAur1.0.100 Hamster  GRCg6a.96 Chicken  Sscrofa11.1.96 Pig or Macaca facicularis 5.0.100 Macaque Supplementary files format and content: h5 or txt files including raw gene – and if present – antibody counts output CellRanger Count Supplementary files format and content: rds file: Seurat object,Liver,,All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.,,shortfilename:CS131|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics – v3|digestion method:Ex Vivo|number of added abs:0|number of cells:1241,GSM5764413,GSM5764413: Zebrafish 002 Whole Liver Cells Zebrafish; Danio rerio; RNA Seq,GSM5764413,,1,All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.,GEO Accession:GSM5764413,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP352824,,,CS131_R1.fastq.gz CS131_R2.fastq.gz,fastq fastq,27410113115.0,230337085.0,GSM5764413 r1,0:28 1:91,A:7502899227;C:6375936516;G:6281396027;T:7241238684;N:8642661,28,91,,,7502899227,6375936516,6281396027,7241238684,8642661,SRX13549231,SRS11443005,SRA1349905,GEO,"VIB Inflammation Research Center, VIB-University of Ghent",2,0.00522,0.93004,0.00164,0.0692,0.99476,0.85098,0.48648,0.60903,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2021-12-29,Undetermined,Undetermined,Liver,Liver and Biliary System
67833,SRR17375071,SRX13549230,SRS11443004,SRP352824,PRJNA793009,Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches single cells,GSE192740,Other,Analysis of CITE seq data   Nuclei RNA seq data and single cell RNA seq data on CD45+ and CD45  cells isolated from the livers of mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar  from healthy and steatotic human livers  from hamster liver  pig liver  chicken liver  monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers  NAFLD mouse livers  healthy human livers and steatotic human livers. Overall design: Single cell RNA Seq = Liver CD45+ and CD45  cells derived from mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar. Liver CD45+ and CD45  cells derived from healthy and obese humans. 10 Visium Spatial Seq = mouse StSt liver  mouse StSt capsule  mouse NAFLD liver   human non steatotic liver  human steatotic liver,parent bioproject:PRJNA793005,pubmed:35021063;pubmed:36304458,,Zebrafish 001 Whole Liver Cells Zebrafish,GSM5764412,,tissue:Liver|shortfilename:CS130|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics – v3|digestion method:Ex Vivo|number of added abs:0|number of cells:2256,Zebrafish 001 Whole Liver Cells Zebrafish,Raw data bcl files were first demultiplexed using Cell Ranger mkfastq version 3.1.0 or version 3.0.2 Demultiplexed data was then processed using the Cell Ranger count pipeline version 3.1.0 or version 3.0.2. Cite seq samples were mapped against the TotalSeqA whitelist. Genome build: mm10 Mouse  hg19 Human  GRCz10 Zebrafish  MesAur1.0.100 Hamster  GRCg6a.96 Chicken  Sscrofa11.1.96 Pig or Macaca facicularis 5.0.100 Macaque Supplementary files format and content: h5 or txt files including raw gene – and if present – antibody counts output CellRanger Count Supplementary files format and content: rds file: Seurat object,Liver,,All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.,,shortfilename:CS130|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics – v3|digestion method:Ex Vivo|number of added abs:0|number of cells:2256,GSM5764412,GSM5764412: Zebrafish 001 Whole Liver Cells Zebrafish; Danio rerio; RNA Seq,GSM5764412,,1,All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.,GEO Accession:GSM5764412,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP352824,,,CS130_R1.fastq.gz CS130_R2.fastq.gz,fastq fastq,29028764681.0,243939199.0,GSM5764412 r1,0:28 1:91,A:7990080958;C:6832189305;G:6802247428;T:7395232074;N:9014916,28,91,,,7990080958,6832189305,6802247428,7395232074,9014916,SRX13549230,SRS11443004,SRA1349905,GEO,"VIB Inflammation Research Center, VIB-University of Ghent",2,0.00621,0.93648,0.00152,0.07051,0.99466,0.85036,0.33907,0.45636,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2021-12-29,Undetermined,Undetermined,Liver,Liver and Biliary System
67834,SRR17375070,SRX13549229,SRS11443003,SRP352824,PRJNA793009,Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches single cells,GSE192740,Other,Analysis of CITE seq data   Nuclei RNA seq data and single cell RNA seq data on CD45+ and CD45  cells isolated from the livers of mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar  from healthy and steatotic human livers  from hamster liver  pig liver  chicken liver  monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers  NAFLD mouse livers  healthy human livers and steatotic human livers. Overall design: Single cell RNA Seq = Liver CD45+ and CD45  cells derived from mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar. Liver CD45+ and CD45  cells derived from healthy and obese humans. 10 Visium Spatial Seq = mouse StSt liver  mouse StSt capsule  mouse NAFLD liver   human non steatotic liver  human steatotic liver,parent bioproject:PRJNA793005,pubmed:35021063;pubmed:36304458,,Zebrafish 002 Liver mpeg1.1+ cells Zebrafish,GSM5764411,,tissue:Liver|shortfilename:CS129|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics – v3|digestion method:Ex Vivo|number of added abs:0|number of cells:4126,Zebrafish 002 Liver mpeg1.1+ cells Zebrafish,Raw data bcl files were first demultiplexed using Cell Ranger mkfastq version 3.1.0 or version 3.0.2 Demultiplexed data was then processed using the Cell Ranger count pipeline version 3.1.0 or version 3.0.2. Cite seq samples were mapped against the TotalSeqA whitelist. Genome build: mm10 Mouse  hg19 Human  GRCz10 Zebrafish  MesAur1.0.100 Hamster  GRCg6a.96 Chicken  Sscrofa11.1.96 Pig or Macaca facicularis 5.0.100 Macaque Supplementary files format and content: h5 or txt files including raw gene – and if present – antibody counts output CellRanger Count Supplementary files format and content: rds file: Seurat object,Liver,,All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.,,shortfilename:CS129|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics – v3|digestion method:Ex Vivo|number of added abs:0|number of cells:4126,GSM5764411,GSM5764411: Zebrafish 002 Liver mpeg1.1+ cells Zebrafish; Danio rerio; RNA Seq,GSM5764411,,1,All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.,GEO Accession:GSM5764411,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP352824,,,CS129_R1.fastq.gz CS129_R2.fastq.gz,fastq fastq,37123150869.0,311959251.0,GSM5764411 r1,0:28 1:91,A:10576275333;C:7976755033;G:8122940005;T:10435522767;N:11657731,28,91,,,10576275333,7976755033,8122940005,10435522767,11657731,SRX13549229,SRS11443003,SRA1349905,GEO,"VIB Inflammation Research Center, VIB-University of Ghent",2,0.00585,0.89093,0.00199,0.20548,0.99269,0.82597,0.42801,0.61509,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2021-12-29,Undetermined,Undetermined,Liver,Liver and Biliary System
67835,SRR17375069,SRX13549228,SRS11443002,SRP352824,PRJNA793009,Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches single cells,GSE192740,Other,Analysis of CITE seq data   Nuclei RNA seq data and single cell RNA seq data on CD45+ and CD45  cells isolated from the livers of mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar  from healthy and steatotic human livers  from hamster liver  pig liver  chicken liver  monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers  NAFLD mouse livers  healthy human livers and steatotic human livers. Overall design: Single cell RNA Seq = Liver CD45+ and CD45  cells derived from mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar. Liver CD45+ and CD45  cells derived from healthy and obese humans. 10 Visium Spatial Seq = mouse StSt liver  mouse StSt capsule  mouse NAFLD liver   human non steatotic liver  human steatotic liver,parent bioproject:PRJNA793005,pubmed:35021063;pubmed:36304458,,Zebrafish 001 Liver mpeg1.1+ cells Zebrafish,GSM5764410,,tissue:Liver|shortfilename:CS128|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics – v3|digestion method:Ex Vivo|number of added abs:0|number of cells:1229,Zebrafish 001 Liver mpeg1.1+ cells Zebrafish,Raw data bcl files were first demultiplexed using Cell Ranger mkfastq version 3.1.0 or version 3.0.2 Demultiplexed data was then processed using the Cell Ranger count pipeline version 3.1.0 or version 3.0.2. Cite seq samples were mapped against the TotalSeqA whitelist. Genome build: mm10 Mouse  hg19 Human  GRCz10 Zebrafish  MesAur1.0.100 Hamster  GRCg6a.96 Chicken  Sscrofa11.1.96 Pig or Macaca facicularis 5.0.100 Macaque Supplementary files format and content: h5 or txt files including raw gene – and if present – antibody counts output CellRanger Count Supplementary files format and content: rds file: Seurat object,Liver,,All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.,,shortfilename:CS128|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics – v3|digestion method:Ex Vivo|number of added abs:0|number of cells:1229,GSM5764410,GSM5764410: Zebrafish 001 Liver mpeg1.1+ cells Zebrafish; Danio rerio; RNA Seq,GSM5764410,,1,All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.,GEO Accession:GSM5764410,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP352824,,,CS128_R1.fastq.gz CS128_R2.fastq.gz,fastq fastq,38316694094.0,321989026.0,GSM5764410 r1,0:28 1:91,A:10814226120;C:8293271134;G:8575797871;T:10621330197;N:12068772,28,91,,,10814226120,8293271134,8575797871,10621330197,12068772,SRX13549228,SRS11443002,SRA1349905,GEO,"VIB Inflammation Research Center, VIB-University of Ghent",2,0.00626,0.88237,0.00215,0.18876,0.99249,0.83049,0.41451,0.59559,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2021-12-29,Undetermined,Undetermined,Liver,Liver and Biliary System
68220,SRR17676758,SRX13840238,SRS11717441,SRP355951,PRJNA798905,Effect of zinc on zerafish brain,GSE194049,Transcriptome Analysis,We evaluated the effect of zinc on zebrafish brain via single cell analysis Overall design: Evaluate the effect of zinc on zebrafish brain via single cell analysis,,,,Zn15 Brain,GSM5827020,,source name:Zn15 Brain Single cell|tissue:Brain|treatment:Zn15,Zn15 Brain,Qualitycontrol We use fastp to perform basic statistics on the quality of the raw reads. Generally  cellranger count support FASTQ files from raw base call BCL files generated by Illumina sequencers as input file. 10x Genomics® not recommend additional processing of the sequence. Generation and Analysis of Single Cell Transcriptomes Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline https://support.10xgenomics.com/single cell geneexpression/software/pipelines/latest/what is cell ranger using default parameters. All downstream single cell analyses were performed using Cell Ranger and Seurat  Macosko et al.  2015; Satija et al.  2015 unless mentioned specifically. In brief  for each gene and each cell barcode filtered by CellRanger  unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed  and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells. Secondary Analysis of Gene Expression cellranger cellranger reanalyze takes feature barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction  clustering  and gene expression algorithms using cellranger default parameter settings Genome build: GRCz11 Supplementary files format and content: barcodes counts  barcodes and gene files,Zn15 Brain Single cell,,Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols,,tissue:Brain|treatment:Zn15,GSM5827020,GSM5827020: Zn15 Brain; Danio rerio; RNA Seq,GSM5827020 r1,GSM5827020,1,Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355951,,,Zinc_1.5-1_S1_L004_R1_001.fastq.gz Zinc_1.5-1_S1_L004_R2_001.fastq.gz,fastq fastq,1539071400.0,5130238.0,GSM5827020 r1,0:150 1:150,A:658313518;C:244042507;G:225665242;T:410991023;N:59110,150,150,,,658313518,244042507,225665242,410991023,59110,SRX13840238,SRS11717441,SRA1359549,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization,2,0.0,0.82858,0.0,0.53324,1.0,0.79498,,0.4737,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-01-20,Undetermined,Undetermined,Brain,Nervous System
68221,SRR17676759,SRX13840238,SRS11717441,SRP355951,PRJNA798905,Effect of zinc on zerafish brain,GSE194049,Transcriptome Analysis,We evaluated the effect of zinc on zebrafish brain via single cell analysis Overall design: Evaluate the effect of zinc on zebrafish brain via single cell analysis,,,,Zn15 Brain,GSM5827020,,source name:Zn15 Brain Single cell|tissue:Brain|treatment:Zn15,Zn15 Brain,Qualitycontrol We use fastp to perform basic statistics on the quality of the raw reads. Generally  cellranger count support FASTQ files from raw base call BCL files generated by Illumina sequencers as input file. 10x Genomics® not recommend additional processing of the sequence. Generation and Analysis of Single Cell Transcriptomes Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline https://support.10xgenomics.com/single cell geneexpression/software/pipelines/latest/what is cell ranger using default parameters. All downstream single cell analyses were performed using Cell Ranger and Seurat  Macosko et al.  2015; Satija et al.  2015 unless mentioned specifically. In brief  for each gene and each cell barcode filtered by CellRanger  unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed  and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells. Secondary Analysis of Gene Expression cellranger cellranger reanalyze takes feature barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction  clustering  and gene expression algorithms using cellranger default parameter settings Genome build: GRCz11 Supplementary files format and content: barcodes counts  barcodes and gene files,Zn15 Brain Single cell,,Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols,,tissue:Brain|treatment:Zn15,GSM5827020,GSM5827020: Zn15 Brain; Danio rerio; RNA Seq,GSM5827020 r1,GSM5827020,1,Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355951,,,Zinc_1.5-2_S1_L004_R1_001.fastq.gz Zinc_1.5-2_S1_L004_R2_001.fastq.gz,fastq fastq,8638750200.0,28795834.0,GSM5827020 r2,0:150 1:150,A:3682612431;C:1369604737;G:1269798921;T:2316421852;N:312259,150,150,,,3682612431,1369604737,1269798921,2316421852,312259,SRX13840238,SRS11717441,SRA1359549,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization,2,0.0,0.83064,0.0,0.5328,1.0,0.79498,,0.47138,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-01-20,Undetermined,Undetermined,Brain,Nervous System
68222,SRR17676760,SRX13840238,SRS11717441,SRP355951,PRJNA798905,Effect of zinc on zerafish brain,GSE194049,Transcriptome Analysis,We evaluated the effect of zinc on zebrafish brain via single cell analysis Overall design: Evaluate the effect of zinc on zebrafish brain via single cell analysis,,,,Zn15 Brain,GSM5827020,,source name:Zn15 Brain Single cell|tissue:Brain|treatment:Zn15,Zn15 Brain,Qualitycontrol We use fastp to perform basic statistics on the quality of the raw reads. Generally  cellranger count support FASTQ files from raw base call BCL files generated by Illumina sequencers as input file. 10x Genomics® not recommend additional processing of the sequence. Generation and Analysis of Single Cell Transcriptomes Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline https://support.10xgenomics.com/single cell geneexpression/software/pipelines/latest/what is cell ranger using default parameters. All downstream single cell analyses were performed using Cell Ranger and Seurat  Macosko et al.  2015; Satija et al.  2015 unless mentioned specifically. In brief  for each gene and each cell barcode filtered by CellRanger  unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed  and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells. Secondary Analysis of Gene Expression cellranger cellranger reanalyze takes feature barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction  clustering  and gene expression algorithms using cellranger default parameter settings Genome build: GRCz11 Supplementary files format and content: barcodes counts  barcodes and gene files,Zn15 Brain Single cell,,Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols,,tissue:Brain|treatment:Zn15,GSM5827020,GSM5827020: Zn15 Brain; Danio rerio; RNA Seq,GSM5827020 r1,GSM5827020,1,Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355951,,,Zinc_1.5-3_S1_L004_R1_001.fastq.gz Zinc_1.5-3_S1_L004_R2_001.fastq.gz,fastq fastq,9587772600.0,31959242.0,GSM5827020 r3,0:150 1:150,A:4074699135;C:1518768107;G:1412325050;T:2581625154;N:355154,150,150,,,4074699135,1518768107,1412325050,2581625154,355154,SRX13840238,SRS11717441,SRA1359549,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization,2,0.0,0.83103,0.0,0.5339,1.0,0.79711,,0.47053,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-01-20,Undetermined,Undetermined,Brain,Nervous System
68223,SRR17676761,SRX13840238,SRS11717441,SRP355951,PRJNA798905,Effect of zinc on zerafish brain,GSE194049,Transcriptome Analysis,We evaluated the effect of zinc on zebrafish brain via single cell analysis Overall design: Evaluate the effect of zinc on zebrafish brain via single cell analysis,,,,Zn15 Brain,GSM5827020,,source name:Zn15 Brain Single cell|tissue:Brain|treatment:Zn15,Zn15 Brain,Qualitycontrol We use fastp to perform basic statistics on the quality of the raw reads. Generally  cellranger count support FASTQ files from raw base call BCL files generated by Illumina sequencers as input file. 10x Genomics® not recommend additional processing of the sequence. Generation and Analysis of Single Cell Transcriptomes Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline https://support.10xgenomics.com/single cell geneexpression/software/pipelines/latest/what is cell ranger using default parameters. All downstream single cell analyses were performed using Cell Ranger and Seurat  Macosko et al.  2015; Satija et al.  2015 unless mentioned specifically. In brief  for each gene and each cell barcode filtered by CellRanger  unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed  and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells. Secondary Analysis of Gene Expression cellranger cellranger reanalyze takes feature barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction  clustering  and gene expression algorithms using cellranger default parameter settings Genome build: GRCz11 Supplementary files format and content: barcodes counts  barcodes and gene files,Zn15 Brain Single cell,,Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols,,tissue:Brain|treatment:Zn15,GSM5827020,GSM5827020: Zn15 Brain; Danio rerio; RNA Seq,GSM5827020 r1,GSM5827020,1,Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355951,,,Zinc_1.5-4_S1_L004_R1_001.fastq.gz Zinc_1.5-4_S1_L004_R2_001.fastq.gz,fastq fastq,8395051500.0,27983505.0,GSM5827020 r4,0:150 1:150,A:3575280442;C:1331736974;G:1234701197;T:2253021609;N:311278,150,150,,,3575280442,1331736974,1234701197,2253021609,311278,SRX13840238,SRS11717441,SRA1359549,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization,2,0.0,0.83011,0.0,0.53379,1.0,0.79766,,0.47537,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-01-20,Undetermined,Undetermined,Brain,Nervous System
68224,SRR17676762,SRX13840237,SRS11717439,SRP355951,PRJNA798905,Effect of zinc on zerafish brain,GSE194049,Transcriptome Analysis,We evaluated the effect of zinc on zebrafish brain via single cell analysis Overall design: Evaluate the effect of zinc on zebrafish brain via single cell analysis,,,,Zn10 Brain,GSM5827019,,source name:Zn10 Brain Single cell|tissue:Brain|treatment:Zn10,Zn10 Brain,Qualitycontrol We use fastp to perform basic statistics on the quality of the raw reads. Generally  cellranger count support FASTQ files from raw base call BCL files generated by Illumina sequencers as input file. 10x Genomics® not recommend additional processing of the sequence. Generation and Analysis of Single Cell Transcriptomes Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline https://support.10xgenomics.com/single cell geneexpression/software/pipelines/latest/what is cell ranger using default parameters. All downstream single cell analyses were performed using Cell Ranger and Seurat  Macosko et al.  2015; Satija et al.  2015 unless mentioned specifically. In brief  for each gene and each cell barcode filtered by CellRanger  unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed  and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells. Secondary Analysis of Gene Expression cellranger cellranger reanalyze takes feature barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction  clustering  and gene expression algorithms using cellranger default parameter settings Genome build: GRCz11 Supplementary files format and content: barcodes counts  barcodes and gene files,Zn10 Brain Single cell,,Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols,,tissue:Brain|treatment:Zn10,GSM5827019,GSM5827019: Zn10 Brain; Danio rerio; RNA Seq,GSM5827019 r1,GSM5827019,1,Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355951,,,Zinc_1.0-1_S1_L004_R2_001.fastq.gz Zinc_1.0-1_S1_L004_R1_001.fastq.gz,fastq fastq,7288135800.0,24293786.0,GSM5827019 r1,0:150 1:150,A:3094809979;C:1153985824;G:1077976879;T:1961096121;N:266997,150,150,,,3094809979,1153985824,1077976879,1961096121,266997,SRX13840237,SRS11717439,SRA1359549,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization,2,0.0,0.82503,0.0,0.50198,1.0,0.7962,,0.46937,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-01-20,Undetermined,Undetermined,Brain,Nervous System
68225,SRR17676763,SRX13840237,SRS11717439,SRP355951,PRJNA798905,Effect of zinc on zerafish brain,GSE194049,Transcriptome Analysis,We evaluated the effect of zinc on zebrafish brain via single cell analysis Overall design: Evaluate the effect of zinc on zebrafish brain via single cell analysis,,,,Zn10 Brain,GSM5827019,,source name:Zn10 Brain Single cell|tissue:Brain|treatment:Zn10,Zn10 Brain,Qualitycontrol We use fastp to perform basic statistics on the quality of the raw reads. Generally  cellranger count support FASTQ files from raw base call BCL files generated by Illumina sequencers as input file. 10x Genomics® not recommend additional processing of the sequence. Generation and Analysis of Single Cell Transcriptomes Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline https://support.10xgenomics.com/single cell geneexpression/software/pipelines/latest/what is cell ranger using default parameters. All downstream single cell analyses were performed using Cell Ranger and Seurat  Macosko et al.  2015; Satija et al.  2015 unless mentioned specifically. In brief  for each gene and each cell barcode filtered by CellRanger  unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed  and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells. Secondary Analysis of Gene Expression cellranger cellranger reanalyze takes feature barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction  clustering  and gene expression algorithms using cellranger default parameter settings Genome build: GRCz11 Supplementary files format and content: barcodes counts  barcodes and gene files,Zn10 Brain Single cell,,Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols,,tissue:Brain|treatment:Zn10,GSM5827019,GSM5827019: Zn10 Brain; Danio rerio; RNA Seq,GSM5827019 r1,GSM5827019,1,Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355951,,,Zinc_1.0-2_S1_L004_R2_001.fastq.gz Zinc_1.0-2_S1_L004_R1_001.fastq.gz,fastq fastq,6934741800.0,23115806.0,GSM5827019 r2,0:150 1:150,A:2965875122;C:1097562270;G:1029305091;T:1841753521;N:245796,150,150,,,2965875122,1097562270,1029305091,1841753521,245796,SRX13840237,SRS11717439,SRA1359549,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization,2,0.0,0.81924,0.0,0.4979,1.0,0.80012,,0.46307,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-01-20,Undetermined,Undetermined,Brain,Nervous System
68226,SRR17676764,SRX13840237,SRS11717439,SRP355951,PRJNA798905,Effect of zinc on zerafish brain,GSE194049,Transcriptome Analysis,We evaluated the effect of zinc on zebrafish brain via single cell analysis Overall design: Evaluate the effect of zinc on zebrafish brain via single cell analysis,,,,Zn10 Brain,GSM5827019,,source name:Zn10 Brain Single cell|tissue:Brain|treatment:Zn10,Zn10 Brain,Qualitycontrol We use fastp to perform basic statistics on the quality of the raw reads. Generally  cellranger count support FASTQ files from raw base call BCL files generated by Illumina sequencers as input file. 10x Genomics® not recommend additional processing of the sequence. Generation and Analysis of Single Cell Transcriptomes Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline https://support.10xgenomics.com/single cell geneexpression/software/pipelines/latest/what is cell ranger using default parameters. All downstream single cell analyses were performed using Cell Ranger and Seurat  Macosko et al.  2015; Satija et al.  2015 unless mentioned specifically. In brief  for each gene and each cell barcode filtered by CellRanger  unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed  and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells. Secondary Analysis of Gene Expression cellranger cellranger reanalyze takes feature barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction  clustering  and gene expression algorithms using cellranger default parameter settings Genome build: GRCz11 Supplementary files format and content: barcodes counts  barcodes and gene files,Zn10 Brain Single cell,,Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols,,tissue:Brain|treatment:Zn10,GSM5827019,GSM5827019: Zn10 Brain; Danio rerio; RNA Seq,GSM5827019 r1,GSM5827019,1,Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355951,,,Zinc_1.0-3_S1_L004_R1_001.fastq.gz Zinc_1.0-3_S1_L004_R2_001.fastq.gz,fastq fastq,8169964500.0,27233215.0,GSM5827019 r3,0:150 1:150,A:3481338543;C:1294858923;G:1206175932;T:2187285678;N:305424,150,150,,,3481338543,1294858923,1206175932,2187285678,305424,SRX13840237,SRS11717439,SRA1359549,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization,2,0.0,0.82416,0.0,0.49999,1.0,0.79472,,0.46866,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-01-20,Undetermined,Undetermined,Brain,Nervous System
68227,SRR17676765,SRX13840237,SRS11717439,SRP355951,PRJNA798905,Effect of zinc on zerafish brain,GSE194049,Transcriptome Analysis,We evaluated the effect of zinc on zebrafish brain via single cell analysis Overall design: Evaluate the effect of zinc on zebrafish brain via single cell analysis,,,,Zn10 Brain,GSM5827019,,source name:Zn10 Brain Single cell|tissue:Brain|treatment:Zn10,Zn10 Brain,Qualitycontrol We use fastp to perform basic statistics on the quality of the raw reads. Generally  cellranger count support FASTQ files from raw base call BCL files generated by Illumina sequencers as input file. 10x Genomics® not recommend additional processing of the sequence. Generation and Analysis of Single Cell Transcriptomes Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline https://support.10xgenomics.com/single cell geneexpression/software/pipelines/latest/what is cell ranger using default parameters. All downstream single cell analyses were performed using Cell Ranger and Seurat  Macosko et al.  2015; Satija et al.  2015 unless mentioned specifically. In brief  for each gene and each cell barcode filtered by CellRanger  unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed  and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells. Secondary Analysis of Gene Expression cellranger cellranger reanalyze takes feature barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction  clustering  and gene expression algorithms using cellranger default parameter settings Genome build: GRCz11 Supplementary files format and content: barcodes counts  barcodes and gene files,Zn10 Brain Single cell,,Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols,,tissue:Brain|treatment:Zn10,GSM5827019,GSM5827019: Zn10 Brain; Danio rerio; RNA Seq,GSM5827019 r1,GSM5827019,1,Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355951,,,Zinc_1.0-4_S1_L004_R2_001.fastq.gz Zinc_1.0-4_S1_L004_R1_001.fastq.gz,fastq fastq,8091230400.0,26970768.0,GSM5827019 r4,0:150 1:150,A:3441274176;C:1280912798;G:1195674942;T:2173061894;N:306590,150,150,,,3441274176,1280912798,1195674942,2173061894,306590,SRX13840237,SRS11717439,SRA1359549,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization,2,0.0,0.82328,0.0,0.50125,1.0,0.79592,,0.46597,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-01-20,Undetermined,Undetermined,Brain,Nervous System
68228,SRR17676766,SRX13840236,SRS11717440,SRP355951,PRJNA798905,Effect of zinc on zerafish brain,GSE194049,Transcriptome Analysis,We evaluated the effect of zinc on zebrafish brain via single cell analysis Overall design: Evaluate the effect of zinc on zebrafish brain via single cell analysis,,,,Ctrl Brain,GSM5827018,,source name:Ctrl Brain Single cell|tissue:Brain|treatment:Ctrl,Ctrl Brain,Qualitycontrol We use fastp to perform basic statistics on the quality of the raw reads. Generally  cellranger count support FASTQ files from raw base call BCL files generated by Illumina sequencers as input file. 10x Genomics® not recommend additional processing of the sequence. Generation and Analysis of Single Cell Transcriptomes Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline https://support.10xgenomics.com/single cell geneexpression/software/pipelines/latest/what is cell ranger using default parameters. All downstream single cell analyses were performed using Cell Ranger and Seurat  Macosko et al.  2015; Satija et al.  2015 unless mentioned specifically. In brief  for each gene and each cell barcode filtered by CellRanger  unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed  and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells. Secondary Analysis of Gene Expression cellranger cellranger reanalyze takes feature barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction  clustering  and gene expression algorithms using cellranger default parameter settings Genome build: GRCz11 Supplementary files format and content: barcodes counts  barcodes and gene files,Ctrl Brain Single cell,,Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols,,tissue:Brain|treatment:Ctrl,GSM5827018,GSM5827018: Ctrl Brain; Danio rerio; RNA Seq,GSM5827018 r1,GSM5827018,1,Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355951,,,Danio_c-1_S1_L004_R1_001.fastq.gz Danio_c-1_S1_L004_R2_001.fastq.gz,fastq fastq,8358635400.0,27862118.0,GSM5827018 r1,0:150 1:150,A:3574888687;C:1303737022;G:1222307199;T:2257382628;N:319864,150,150,,,3574888687,1303737022,1222307199,2257382628,319864,SRX13840236,SRS11717440,SRA1359549,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization,2,0.0,0.82441,0.0,0.52105,1.0,0.79985,,0.46893,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-01-20,Undetermined,Undetermined,Brain,Nervous System