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
25228,SRR25685572,SRX21410761,SRS18649243,SRP455780,PRJNA1006660,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish],GSE241156,Other,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,zebrafish 14dpi heart3,GSM7717530,,source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi|geo loc name:missing|collection date:missing,zebrafish 14dpi heart3,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish,adult heart,Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi,GSM7717530,GSM7717530: zebrafish 14dpi heart3; Danio rerio; RNA Seq,GSM7717530 r1,GSM7717530,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,loader:fastq load.py|options:  allowEarlyFileEnd,DB14zf4_R1.fq DB14zf4_R2.fq,fastq fastq,571157496.0,7312520.0,GSM7717530 r1,,A:132329616;C:53169305;G:72431948;T:313058610;N:168017,,,,,132329616,53169305,72431948,313058610,168017,SRX21410761,SRS18649243,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.01414,0.679,0.01413,0.08289,1.0,0.98395,,0.48915,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25229,SRR25685573,SRX21410760,SRS18649241,SRP455780,PRJNA1006660,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish],GSE241156,Other,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,zebrafish 14dpi heart2,GSM7717529,,source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi|geo loc name:missing|collection date:missing,zebrafish 14dpi heart2,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish,adult heart,Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi,GSM7717529,GSM7717529: zebrafish 14dpi heart2; Danio rerio; RNA Seq,GSM7717529 r1,GSM7717529,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,loader:fastq load.py|options:  allowEarlyFileEnd,DB14zf3_R1.fq DB14zf3_R2.fq,fastq fastq,97890367.0,1292037.0,GSM7717529 r1,,A:21637243;C:8563955;G:12004508;T:55662880;N:21781,,,,,21637243,8563955,12004508,55662880,21781,SRX21410760,SRS18649241,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.0,0.689,0.0,0.07655,1.0,0.99831,,0.63709,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25230,SRR25685574,SRX21410759,SRS18649242,SRP455780,PRJNA1006660,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish],GSE241156,Other,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,zebrafish 14dpi heart1,GSM7717528,,source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi|geo loc name:missing|collection date:missing,zebrafish 14dpi heart1,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish,adult heart,Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi,GSM7717528,GSM7717528: zebrafish 14dpi heart1; Danio rerio; RNA Seq,GSM7717528 r1,GSM7717528,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,loader:fastq load.py|options:  allowEarlyFileEnd,DB14zf1_R1.fq DB14zf1_R2.fq,fastq fastq,1031757474.0,7257847.0,GSM7717528 r1,,A:276216587;C:146620316;G:184052670;T:423474577;N:1393324,,,,,276216587,146620316,184052670,423474577,1393324,SRX21410759,SRS18649242,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.04176,0.6198,0.03023,0.08234,0.99894,0.88885,0.64556,0.53126,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25231,SRR25685575,SRX21410758,SRS18649240,SRP455780,PRJNA1006660,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish],GSE241156,Other,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,zebrafish 7dpi heart3,GSM7717527,,source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi|geo loc name:missing|collection date:missing,zebrafish 7dpi heart3,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish,adult heart,Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi,GSM7717527,GSM7717527: zebrafish 7dpi heart3; Danio rerio; RNA Seq,GSM7717527 r1,GSM7717527,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,loader:fastq load.py|options:  allowEarlyFileEnd,D37DPIZF3_R1.fq D37DPIZF3_R2.fq,fastq fastq,898901460.0,7585924.0,GSM7717527 r1,,A:236935836;C:100995680;G:128458892;T:431620821;N:890231,,,,,236935836,100995680,128458892,431620821,890231,SRX21410758,SRS18649240,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.12082,0.70068,0.10594,0.1234,0.99983,0.90136,0.875,0.48346,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25232,SRR25685576,SRX21410757,SRS18649239,SRP455780,PRJNA1006660,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish],GSE241156,Other,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,zebrafish 7dpi heart2,GSM7717526,,source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi|geo loc name:missing|collection date:missing,zebrafish 7dpi heart2,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish,adult heart,Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi,GSM7717526,GSM7717526: zebrafish 7dpi heart2; Danio rerio; RNA Seq,GSM7717526 r1,GSM7717526,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,loader:fastq load.py|options:  allowEarlyFileEnd,D27DPIZF2_R1.fq D27DPIZF2_R2.fq,fastq fastq,1060429257.0,7609110.0,GSM7717526 r1,,A:283107752;C:130181128;G:159305328;T:486464477;N:1370572,,,,,283107752,130181128,159305328,486464477,1370572,SRX21410757,SRS18649239,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.19472,0.68783,0.17584,0.16739,0.99967,0.85628,0.44,0.56319,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25233,SRR25685577,SRX21410756,SRS18649238,SRP455780,PRJNA1006660,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish],GSE241156,Other,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,zebrafish 7dpi heart1,GSM7717525,,source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi|geo loc name:missing|collection date:missing,zebrafish 7dpi heart1,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish,adult heart,Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi,GSM7717525,GSM7717525: zebrafish 7dpi heart1; Danio rerio; RNA Seq,GSM7717525 r1,GSM7717525,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,loader:fastq load.py|options:  allowEarlyFileEnd,D17DPIZF1_R1.fq D17DPIZF1_R2.fq,fastq fastq,1073044507.0,7624815.0,GSM7717525 r1,,A:288576038;C:136858647;G:170330711;T:475869519;N:1409592,,,,,288576038,136858647,170330711,475869519,1409592,SRX21410756,SRS18649238,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.15938,0.70435,0.14583,0.08079,0.99981,0.87949,0.38461,0.57027,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25234,SRR25685578,SRX21410755,SRS18649237,SRP455780,PRJNA1006660,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish],GSE241156,Other,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,zebrafish 3dpi heart3,GSM7717524,,source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi|geo loc name:missing|collection date:missing,zebrafish 3dpi heart3,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish,adult heart,Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi,GSM7717524,GSM7717524: zebrafish 3dpi heart3; Danio rerio; RNA Seq,GSM7717524 r1,GSM7717524,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,,FKHEART3_R1.fastq FKHEART3_R2.fastq,fastq fastq,781079621.0,5184230.0,GSM7717524 r1,0:75.26 1:75.40,A:277491111;C:118539142;G:116911958;T:268048500;N:88910,75,75,,,277491111,118539142,116911958,268048500,88910,SRX21410755,SRS18649237,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.04348,0.71869,0.04347,0.28823,1.0,0.79681,,0.53909,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25235,SRR25685579,SRX21410754,SRS18649236,SRP455780,PRJNA1006660,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish],GSE241156,Other,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,zebrafish 3dpi heart2,GSM7717523,,source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi|geo loc name:missing|collection date:missing,zebrafish 3dpi heart2,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish,adult heart,Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi,GSM7717523,GSM7717523: zebrafish 3dpi heart2; Danio rerio; RNA Seq,GSM7717523 r1,GSM7717523,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,,FKHEART2_R1.fastq FKHEART2_R2.fastq,fastq fastq,684820059.0,4547520.0,GSM7717523 r1,0:75.21 1:75.38,A:258487418;C:93776953;G:97187917;T:235293267;N:74504,75,75,,,258487418,93776953,97187917,235293267,74504,SRX21410754,SRS18649236,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.09406,0.79542,0.09405,0.0802,1.0,0.83029,,0.56367,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25236,SRR25685580,SRX21410753,SRS18649235,SRP455780,PRJNA1006660,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish],GSE241156,Other,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,zebrafish 3dpi heart1,GSM7717522,,source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi|geo loc name:missing|collection date:missing,zebrafish 3dpi heart1,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish,adult heart,Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi,GSM7717522,GSM7717522: zebrafish 3dpi heart1; Danio rerio; RNA Seq,GSM7717522 r1,GSM7717522,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,,FKHEART1_R1.fastq FKHEART1_R2.fastq,fastq fastq,784558404.0,5209213.0,GSM7717522 r1,0:75.22 1:75.39,A:291009319;C:102718146;G:111606154;T:279144074;N:80711,75,75,,,291009319,102718146,111606154,279144074,80711,SRX21410753,SRS18649235,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.13119,0.82035,0.12871,0.08445,0.99997,0.82785,0.0,0.56254,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25239,SRR25723792,SRX21447930,SRS18684553,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 4,GSM7728123,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 4,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728123,GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq,GSM7728123 r1,GSM7728123,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-008_HNWVVBGX9_S7_L001_R2_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L001_R1_001.fastq.gz,fastq fastq,529790530.0,6160355.0,GSM7728123 r1,0:26 1:60,A:134254092;C:100685793;G:108463112;T:186279563;N:107970,26,60,,,134254092,100685793,108463112,186279563,107970,SRX21447930,SRS18684553,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11277,0.80912,0.10457,0.43275,0.99131,0.93933,0.67026,0.54274,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25240,SRR25723793,SRX21447930,SRS18684553,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 4,GSM7728123,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 4,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728123,GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq,GSM7728123 r1,GSM7728123,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-008_HNWVVBGX9_S7_L002_R1_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L002_R2_001.fastq.gz,fastq fastq,611015122.0,7104827.0,GSM7728123 r2,0:26 1:60,A:152137832;C:116026517;G:127735448;T:214967198;N:148127,26,60,,,152137832,116026517,127735448,214967198,148127,SRX21447930,SRS18684553,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11413,0.81785,0.10565,0.44205,0.99119,0.93419,0.59743,0.53882,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25241,SRR25723794,SRX21447930,SRS18684553,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 4,GSM7728123,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 4,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728123,GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq,GSM7728123 r1,GSM7728123,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-008_HNWVVBGX9_S7_L003_R2_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L003_R1_001.fastq.gz,fastq fastq,554981822.0,6453277.0,GSM7728123 r3,0:26 1:60,A:140664360;C:105281601;G:113575873;T:195359632;N:100356,26,60,,,140664360,105281601,113575873,195359632,100356,SRX21447930,SRS18684553,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11352,0.80651,0.10538,0.42971,0.99137,0.93994,0.65893,0.53098,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25242,SRR25723795,SRX21447930,SRS18684553,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 4,GSM7728123,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 4,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728123,GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq,GSM7728123 r1,GSM7728123,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-008_HNWVVBGX9_S7_L004_R2_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L004_R1_001.fastq.gz,fastq fastq,459861436.0,5347226.0,GSM7728123 r4,0:26 1:60,A:115949245;C:86913961;G:95720860;T:161187969;N:89401,26,60,,,115949245,86913961,95720860,161187969,89401,SRX21447930,SRS18684553,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11249,0.81109,0.10407,0.43334,0.99135,0.94034,0.64852,0.53864,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25243,SRR25723796,SRX21447929,SRS18684552,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 3,GSM7728122,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 3,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728122,GSM7728122: hmga1a mutant plate 3; Danio rerio; RNA Seq,GSM7728122 r1,GSM7728122,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-007_HNWVVBGX9_S6_L001_R1_001.fastq.gz HUB-DB-007_HNWVVBGX9_S6_L001_R2_001.fastq.gz,fastq fastq,584059454.0,6791389.0,GSM7728122 r1,0:26 1:60,A:162038298;C:107975394;G:118251259;T:195669218;N:125285,26,60,,,162038298,107975394,118251259,195669218,125285,SRX21447929,SRS18684552,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.08872,0.68673,0.08328,0.37858,0.99346,0.94945,0.60282,0.42608,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25244,SRR25723797,SRX21447929,SRS18684552,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 3,GSM7728122,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 3,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728122,GSM7728122: hmga1a mutant plate 3; Danio rerio; RNA Seq,GSM7728122 r1,GSM7728122,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-007_HNWVVBGX9_S6_L002_R1_001.fastq.gz HUB-DB-007_HNWVVBGX9_S6_L002_R2_001.fastq.gz,fastq fastq,641359448.0,7457668.0,GSM7728122 r2,0:26 1:60,A:174443468;C:118438230;G:132604485;T:215721538;N:151727,26,60,,,174443468,118438230,132604485,215721538,151727,SRX21447929,SRS18684552,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.09277,0.71427,0.08722,0.3942,0.99338,0.94594,0.56903,0.45872,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25245,SRR25723798,SRX21447929,SRS18684552,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 3,GSM7728122,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 3,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728122,GSM7728122: hmga1a mutant plate 3; Danio rerio; RNA Seq,GSM7728122 r1,GSM7728122,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-007_HNWVVBGX9_S6_L003_R1_001.fastq.gz HUB-DB-007_HNWVVBGX9_S6_L003_R2_001.fastq.gz,fastq fastq,609857046.0,7091361.0,GSM7728122 r3,0:26 1:60,A:169007241;C:112556048;G:123345017;T:204831635;N:117105,26,60,,,169007241,112556048,123345017,204831635,117105,SRX21447929,SRS18684552,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.09058,0.68251,0.08521,0.37718,0.99332,0.95156,0.59403,0.44605,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25246,SRR25723799,SRX21447929,SRS18684552,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 3,GSM7728122,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 3,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728122,GSM7728122: hmga1a mutant plate 3; Danio rerio; RNA Seq,GSM7728122 r1,GSM7728122,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-007_HNWVVBGX9_S6_L004_R1_001.fastq.gz HUB-DB-007_HNWVVBGX9_S6_L004_R2_001.fastq.gz,fastq fastq,514759966.0,5985581.0,GSM7728122 r4,0:26 1:60,A:142060859;C:94579961;G:106100208;T:171916257;N:102681,26,60,,,142060859,94579961,106100208,171916257,102681,SRX21447929,SRS18684552,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.08962,0.7176,0.08411,0.39394,0.99293,0.95189,0.55398,0.46149,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25247,SRR25723800,SRX21447928,SRS18684551,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,wildtype plate 3,GSM7728121,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,wildtype plate 3,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728121,GSM7728121: wildtype plate 3; Danio rerio; RNA Seq,GSM7728121 r1,GSM7728121,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-006_HNWVVBGX9_S5_L001_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L001_R2_001.fastq.gz,fastq fastq,929999528.0,10813948.0,GSM7728121 r1,0:26 1:60,A:240334465;C:174255952;G:184260587;T:330943403;N:205121,26,60,,,240334465,174255952,184260587,330943403,205121,SRX21447928,SRS18684551,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11113,0.87407,0.10304,0.43976,0.992,0.93034,0.63031,0.44624,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25248,SRR25723801,SRX21447928,SRS18684551,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,wildtype plate 3,GSM7728121,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,wildtype plate 3,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728121,GSM7728121: wildtype plate 3; Danio rerio; RNA Seq,GSM7728121 r1,GSM7728121,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-006_HNWVVBGX9_S5_L002_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L002_R2_001.fastq.gz,fastq fastq,987824896.0,11486336.0,GSM7728121 r2,0:26 1:60,A:251121714;C:184449811;G:201317783;T:350692225;N:243363,26,60,,,251121714,184449811,201317783,350692225,243363,SRX21447928,SRS18684551,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11267,0.87874,0.10429,0.4457,0.99184,0.92498,0.56612,0.45489,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25249,SRR25723802,SRX21447928,SRS18684551,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,wildtype plate 3,GSM7728121,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,wildtype plate 3,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728121,GSM7728121: wildtype plate 3; Danio rerio; RNA Seq,GSM7728121 r1,GSM7728121,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-006_HNWVVBGX9_S5_L003_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L003_R2_001.fastq.gz,fastq fastq,959933032.0,11162012.0,GSM7728121 r3,0:26 1:60,A:247983556;C:179564753;G:190342582;T:341858456;N:183685,26,60,,,247983556,179564753,190342582,341858456,183685,SRX21447928,SRS18684551,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.1118,0.87156,0.10348,0.43983,0.99149,0.93034,0.65287,0.44548,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25250,SRR25723803,SRX21447928,SRS18684551,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,wildtype plate 3,GSM7728121,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,wildtype plate 3,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728121,GSM7728121: wildtype plate 3; Danio rerio; RNA Seq,GSM7728121 r1,GSM7728121,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-006_HNWVVBGX9_S5_L004_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L004_R2_001.fastq.gz,fastq fastq,798370766.0,9283381.0,GSM7728121 r4,0:26 1:60,A:205538880;C:148510556;G:161196381;T:282964175;N:160774,26,60,,,205538880,148510556,161196381,282964175,160774,SRX21447928,SRS18684551,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11018,0.87017,0.10214,0.43625,0.99226,0.93332,0.56058,0.44211,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25251,SRR25723804,SRX21447927,SRS18684550,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,wildtype plate 2,GSM7728120,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,wildtype plate 2,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728120,GSM7728120: wildtype plate 2; Danio rerio; RNA Seq,GSM7728120 r1,GSM7728120,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-005_HNWVVBGX9_S4_L001_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L001_R2_001.fastq.gz,fastq fastq,806178534.0,9374169.0,GSM7728120 r1,0:26 1:60,A:213590554;C:148614157;G:163804315;T:279996916;N:172592,26,60,,,213590554,148614157,163804315,279996916,172592,SRX21447927,SRS18684550,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10778,0.79219,0.10092,0.39443,0.99255,0.93712,0.64412,0.39504,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25252,SRR25723805,SRX21447927,SRS18684550,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,wildtype plate 2,GSM7728120,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,wildtype plate 2,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728120,GSM7728120: wildtype plate 2; Danio rerio; RNA Seq,GSM7728120 r1,GSM7728120,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-005_HNWVVBGX9_S4_L002_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L002_R2_001.fastq.gz,fastq fastq,874594286.0,10169701.0,GSM7728120 r2,0:26 1:60,A:227213153;C:160851586;G:182364146;T:303951184;N:214217,26,60,,,227213153,160851586,182364146,303951184,214217,SRX21447927,SRS18684550,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11064,0.80317,0.1038,0.40093,0.99249,0.9332,0.652,0.40914,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25253,SRR25723806,SRX21447927,SRS18684550,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,wildtype plate 2,GSM7728120,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,wildtype plate 2,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728120,GSM7728120: wildtype plate 2; Danio rerio; RNA Seq,GSM7728120 r1,GSM7728120,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-005_HNWVVBGX9_S4_L003_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L003_R2_001.fastq.gz,fastq fastq,831835860.0,9672510.0,GSM7728120 r3,0:26 1:60,A:220300204;C:153061412;G:168938657;T:289375449;N:160138,26,60,,,220300204,153061412,168938657,289375449,160138,SRX21447927,SRS18684550,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10987,0.78665,0.10348,0.39264,0.99316,0.93661,0.66753,0.37676,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25254,SRR25723807,SRX21447927,SRS18684550,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,wildtype plate 2,GSM7728120,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,wildtype plate 2,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728120,GSM7728120: wildtype plate 2; Danio rerio; RNA Seq,GSM7728120 r1,GSM7728120,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-005_HNWVVBGX9_S4_L004_R2_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L004_R1_001.fastq.gz,fastq fastq,692573136.0,8053176.0,GSM7728120 r4,0:26 1:60,A:182418113;C:126757471;G:143869511;T:239393143;N:134898,26,60,,,182418113,126757471,143869511,239393143,134898,SRX21447927,SRS18684550,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10825,0.81365,0.10178,0.40513,0.99308,0.94032,0.67299,0.41125,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25255,SRR25723808,SRX21447926,SRS18684549,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 2,GSM7728119,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 2,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728119,GSM7728119: hmga1a mutant plate 2; Danio rerio; RNA Seq,GSM7728119 r1,GSM7728119,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-004_AHVKTGBGX7_S7_L001_R1_001.fastq.gz HUB-DB-004_AHVKTGBGX7_S7_L001_R2_001.fastq.gz,fastq fastq,364147736.0,4234276.0,GSM7728119 r1,0:26 1:60,A:94538754;C:69024492;G:68361658;T:132108181;N:114651,26,60,,,94538754,69024492,68361658,132108181,114651,SRX21447926,SRS18684549,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11558,0.78278,0.10659,0.24226,0.9893,0.92719,0.58692,0.48105,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25256,SRR25723809,SRX21447926,SRS18684549,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 2,GSM7728119,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 2,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728119,GSM7728119: hmga1a mutant plate 2; Danio rerio; RNA Seq,GSM7728119 r1,GSM7728119,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-004_AHVKTGBGX7_S7_L002_R1_001.fastq.gz HUB-DB-004_AHVKTGBGX7_S7_L002_R2_001.fastq.gz,fastq fastq,377653262.0,4391317.0,GSM7728119 r2,0:26 1:60,A:99999342;C:71104204;G:70005970;T:136434888;N:108858,26,60,,,99999342,71104204,70005970,136434888,108858,SRX21447926,SRS18684549,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11405,0.77996,0.10525,0.24008,0.98963,0.93616,0.60855,0.44129,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25257,SRR25723810,SRX21447926,SRS18684549,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 2,GSM7728119,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 2,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728119,GSM7728119: hmga1a mutant plate 2; Danio rerio; RNA Seq,GSM7728119 r1,GSM7728119,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-004_AHVKTGBGX7_S7_L003_R1_001.fastq.gz HUB-DB-004_AHVKTGBGX7_S7_L003_R2_001.fastq.gz,fastq fastq,306947588.0,3569158.0,GSM7728119 r3,0:26 1:60,A:80261116;C:58220837;G:57196503;T:111195958;N:73174,26,60,,,80261116,58220837,57196503,111195958,73174,SRX21447926,SRS18684549,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11141,0.76713,0.10254,0.23772,0.98938,0.93314,0.62261,0.47885,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25258,SRR25723811,SRX21447926,SRS18684549,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 2,GSM7728119,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 2,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728119,GSM7728119: hmga1a mutant plate 2; Danio rerio; RNA Seq,GSM7728119 r1,GSM7728119,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-004_AHVKTGBGX7_S7_L004_R1_001.fastq.gz HUB-DB-004_AHVKTGBGX7_S7_L004_R2_001.fastq.gz,fastq fastq,389472414.0,4528749.0,GSM7728119 r4,0:26 1:60,A:102486709;C:73105388;G:73019179;T:140769931;N:91207,26,60,,,102486709,73105388,73019179,140769931,91207,SRX21447926,SRS18684549,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11502,0.78307,0.10673,0.24219,0.98967,0.93308,0.64527,0.43659,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25259,SRR25723812,SRX21447925,SRS18684547,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 1,GSM7728118,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 1,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728118,GSM7728118: hmga1a mutant plate 1; Danio rerio; RNA Seq,GSM7728118 r1,GSM7728118,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-003_AHVKTGBGX7_S6_L001_R1_001.fastq.gz HUB-DB-003_AHVKTGBGX7_S6_L001_R2_001.fastq.gz,fastq fastq,381365624.0,4434484.0,GSM7728118 r1,0:26 1:60,A:102130758;C:71032768;G:73641442;T:134437630;N:123026,26,60,,,102130758,71032768,73641442,134437630,123026,SRX21447925,SRS18684547,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10052,0.7243,0.09214,0.25633,0.9892,0.92985,0.52345,0.5112,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25260,SRR25723813,SRX21447925,SRS18684547,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 1,GSM7728118,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 1,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728118,GSM7728118: hmga1a mutant plate 1; Danio rerio; RNA Seq,GSM7728118 r1,GSM7728118,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-003_AHVKTGBGX7_S6_L002_R1_001.fastq.gz HUB-DB-003_AHVKTGBGX7_S6_L002_R2_001.fastq.gz,fastq fastq,400525220.0,4657270.0,GSM7728118 r2,0:26 1:60,A:109307778;C:73934198;G:76916762;T:140249156;N:117326,26,60,,,109307778,73934198,76916762,140249156,117326,SRX21447925,SRS18684547,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.09923,0.71601,0.09078,0.25139,0.98948,0.93914,0.52314,0.5078,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25261,SRR25723814,SRX21447925,SRS18684547,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 1,GSM7728118,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 1,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728118,GSM7728118: hmga1a mutant plate 1; Danio rerio; RNA Seq,GSM7728118 r1,GSM7728118,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-003_AHVKTGBGX7_S6_L003_R1_001.fastq.gz HUB-DB-003_AHVKTGBGX7_S6_L003_R2_001.fastq.gz,fastq fastq,341364014.0,3969349.0,GSM7728118 r3,0:26 1:60,A:91716565;C:63676514;G:65563102;T:120323617;N:84216,26,60,,,91716565,63676514,65563102,120323617,84216,SRX21447925,SRS18684547,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.09826,0.7079,0.09008,0.2497,0.98918,0.93809,0.52649,0.49781,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25262,SRR25723815,SRX21447925,SRS18684547,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 1,GSM7728118,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 1,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728118,GSM7728118: hmga1a mutant plate 1; Danio rerio; RNA Seq,GSM7728118 r1,GSM7728118,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-003_AHVKTGBGX7_S6_L004_R1_001.fastq.gz HUB-DB-003_AHVKTGBGX7_S6_L004_R2_001.fastq.gz,fastq fastq,414000732.0,4813962.0,GSM7728118 r4,0:26 1:60,A:112224009;C:76213738;G:80259829;T:145201785;N:101371,26,60,,,112224009,76213738,80259829,145201785,101371,SRX21447925,SRS18684547,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10103,0.71981,0.09294,0.25413,0.98902,0.93669,0.52994,0.51172,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25263,SRR25723816,SRX21447924,SRS18684548,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,wildtype plate 1,GSM7728117,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,wildtype plate 1,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728117,GSM7728117: wildtype plate 1; Danio rerio; RNA Seq,GSM7728117 r1,GSM7728117,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-001_AHVKTGBGX7_S5_L001_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L001_R2_001.fastq.gz,fastq fastq,471703034.0,5484919.0,GSM7728117 r1,0:26 1:60,A:125045012;C:89627491;G:85413855;T:171466861;N:149815,26,60,,,125045012,89627491,85413855,171466861,149815,SRX21447924,SRS18684548,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10906,0.68002,0.10212,0.30506,0.99101,0.94219,0.63738,0.45862,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25264,SRR25723817,SRX21447924,SRS18684548,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,wildtype plate 1,GSM7728117,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,wildtype plate 1,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728117,GSM7728117: wildtype plate 1; Danio rerio; RNA Seq,GSM7728117 r1,GSM7728117,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-001_AHVKTGBGX7_S5_L002_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L002_R2_001.fastq.gz,fastq fastq,489372938.0,5690383.0,GSM7728117 r2,0:26 1:60,A:131516821;C:92202683;G:88685608;T:176824985;N:142841,26,60,,,131516821,92202683,88685608,176824985,142841,SRX21447924,SRS18684548,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11042,0.68086,0.10299,0.30411,0.99093,0.94856,0.60224,0.46578,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25265,SRR25723818,SRX21447924,SRS18684548,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,wildtype plate 1,GSM7728117,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,wildtype plate 1,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728117,GSM7728117: wildtype plate 1; Danio rerio; RNA Seq,GSM7728117 r1,GSM7728117,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-001_AHVKTGBGX7_S5_L003_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L003_R2_001.fastq.gz,fastq fastq,407735288.0,4741108.0,GSM7728117 r3,0:26 1:60,A:108841476;C:77418215;G:73171345;T:148203998;N:100254,26,60,,,108841476,77418215,73171345,148203998,100254,SRX21447924,SRS18684548,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10882,0.67068,0.10177,0.29557,0.99151,0.94686,0.65762,0.42658,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25266,SRR25723819,SRX21447924,SRS18684548,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,wildtype plate 1,GSM7728117,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,wildtype plate 1,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728117,GSM7728117: wildtype plate 1; Danio rerio; RNA Seq,GSM7728117 r1,GSM7728117,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-001_AHVKTGBGX7_S5_L004_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L004_R2_001.fastq.gz,fastq fastq,505539304.0,5878364.0,GSM7728117 r4,0:26 1:60,A:135189083;C:94908231;G:92431583;T:182885125;N:125282,26,60,,,135189083,94908231,92431583,182885125,125282,SRX21447924,SRS18684548,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10989,0.68603,0.10286,0.30542,0.99107,0.94777,0.65338,0.42121,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
38073,SRR1531483,SRX665263,SRS670077,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,18 somites stage  straightened  secti1d tail to head,GSM1448820,,tissue:deyolked embryo  head removed|Stage:18 somites|sectioning direction:tail to head|section thickness:24 µm|embedding strategy:deyolked and straightened embryo,18 somites stage  straightened  secti1d tail to head,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,deyolked embryo  head removed,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:18 somites|sectioning direction:tail to head|section thickness:24 µm|embedding strategy:deyolked and straightened embryo,GSM1448820,GSM1448820: 18 somites stage  straightened  secti1d tail to head; Danio rerio; RNA Seq,GSM1448820,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448820,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_18ss_TH_R2.fastq.gz dr_18ss_TH_R1.fastq.gz,fastq fastq,15779230884.0,154698342.0,GSM1448820 r1,0:51 1:51,A:3451000604;C:2392800593;G:2522666152;T:7412137093;N:626442,51,51,,,3451000604,2392800593,2522666152,7412137093,626442,SRX665263,SRS670077,SRA177126,GEO,Hubrecht Institute,2,0.11555,0.70031,0.08647,0.12212,0.98238,0.78946,0.48905,0.5514,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
38074,SRR1531482,SRX665262,SRS670076,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somites stage  straightened  secti1d tail to head  replicate,GSM1448819,,tissue:deyolked embryo|Stage:15 somites|sectioning direction:tail to head|section thickness:18 µm|embedding strategy:deyolked and straightened embryo,15 somites stage  straightened  secti1d tail to head  replicate,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,deyolked embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:tail to head|section thickness:18 µm|embedding strategy:deyolked and straightened embryo,GSM1448819,GSM1448819: 15 somites stage  straightened  secti1d tail to head  replicate; Danio rerio; RNA Seq,GSM1448819,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448819,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_15ss_TH2_R2.fastq.gz dr_15ss_TH2_R1.fastq.gz,fastq fastq,4502603442.0,44143171.0,GSM1448819 r1,0:51 1:51,A:1010801791;C:688133305;G:712006267;T:2047960758;N:43701321,51,51,,,1010801791,688133305,712006267,2047960758,43701321,SRX665262,SRS670076,SRA177126,GEO,Hubrecht Institute,2,0.0903,0.78618,0.08054,0.12953,0.98703,0.78046,0.53574,0.52775,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
38075,SRR1531481,SRX665261,SRS670075,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,sections 97 108 for samples dr 15ss TH and dr 15ss HT,GSM1448818,,tissue:deyolked embryo|Stage:15 somites|sectioning direction:head to tail and tail to head|section thickness:18 µm|embedding strategy:deyolked and straightened embryo,sections 97 108 for samples dr 15ss TH and dr 15ss HT,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,deyolked embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:head to tail and tail to head|section thickness:18 µm|embedding strategy:deyolked and straightened embryo,GSM1448818,GSM1448818: sections 97 108 for samples dr 15ss TH and dr 15ss HT; Danio rerio; RNA Seq,GSM1448818,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448818,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_15ss_TH97-108_HT97-108_R2.fastq.gz dr_15ss_TH97-108_HT97-108_R1.fastq.gz,fastq fastq,472071606.0,4628153.0,GSM1448818 r1,0:51 1:51,A:108013079;C:76852222;G:73612321;T:208300498;N:5293486,51,51,,,108013079,76852222,73612321,208300498,5293486,SRX665261,SRS670075,SRA177126,GEO,Hubrecht Institute,2,0.06997,0.71056,0.06103,0.12966,0.9865,0.79446,0.53118,0.53673,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
38076,SRR1531480,SRX665260,SRS670074,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somites stage  straightened  secti1d tail to head,GSM1448817,,tissue:deyolked embryo|Stage:15 somites|sectioning direction:tail to head|section thickness:18 µm|embedding strategy:deyolked and straightened embryo,15 somites stage  straightened  secti1d tail to head,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,deyolked embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:tail to head|section thickness:18 µm|embedding strategy:deyolked and straightened embryo,GSM1448817,GSM1448817: 15 somites stage  straightened  secti1d tail to head; Danio rerio; RNA Seq,GSM1448817,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448817,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_15ss_TH_R1.fastq.gz dr_15ss_TH_R2.fastq.gz,fastq fastq,3381229314.0,33149307.0,GSM1448817 r1,0:51 1:51,A:806003850;C:517726785;G:527487361;T:1491678004;N:38333314,51,51,,,806003850,517726785,527487361,1491678004,38333314,SRX665260,SRS670074,SRA177126,GEO,Hubrecht Institute,2,0.06812,0.69273,0.05849,0.1511,0.98502,0.7834,0.47808,0.53868,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
38077,SRR1531479,SRX665259,SRS670073,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somites stage  straightened  secti1d head to tail,GSM1448816,,tissue:deyolked embryo|Stage:15 somites|sectioning direction:head to tail|section thickness:18 µm|embedding strategy:deyolked and straightened embryo,15 somites stage  straightened  secti1d head to tail,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,deyolked embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:head to tail|section thickness:18 µm|embedding strategy:deyolked and straightened embryo,GSM1448816,GSM1448816: 15 somites stage  straightened  secti1d head to tail; Danio rerio; RNA Seq,GSM1448816,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448816,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_15ss_HT_R1.fastq.gz dr_15ss_HT_R2.fastq.gz,fastq fastq,3476174076.0,34080138.0,GSM1448816 r1,0:51 1:51,A:800519794;C:540890287;G:554165272;T:1542680760;N:37917963,51,51,,,800519794,540890287,554165272,1542680760,37917963,SRX665259,SRS670073,SRA177126,GEO,Hubrecht Institute,2,0.06769,0.70036,0.05945,0.13184,0.98849,0.79026,0.50058,0.57003,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
38078,SRR1531477,SRX665258,SRS670072,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from right to left,GSM1448815,,tissue:whole embryo|Stage:15 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from right to left,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,GSM1448815,GSM1448815: 15 somite stage  secti1d from right to left; Danio rerio; RNA Seq,GSM1448815,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448815,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_15ss_RL_R1.fastq.gz dr_15ss_RL_R2.fastq.gz,fastq fastq,3840123336.0,37648268.0,GSM1448815 r1,0:51 1:51,A:915153174;C:577478134;G:648196113;T:1695635476;N:3660439,51,51,,,915153174,577478134,648196113,1695635476,3660439,SRX665258,SRS670072,SRA177126,GEO,Hubrecht Institute,2,0.05313,0.71589,0.0419,0.15174,0.97717,0.77484,0.5218,0.45828,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38079,SRR1531478,SRX665258,SRS670072,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from right to left,GSM1448815,,tissue:whole embryo|Stage:15 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from right to left,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,GSM1448815,GSM1448815: 15 somite stage  secti1d from right to left; Danio rerio; RNA Seq,GSM1448815,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448815,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_15ss_RL_R1.fastq.gz miseq_dr_15ss_RL_R2.fastq.gz,fastq fastq,619303490.0,1235999.0,GSM1448815 r2,0:251 1:250.06,A:196814024;C:126079066;G:111585151;T:184825248;N:1,251,250,,,196814024,126079066,111585151,184825248,1,SRX665258,SRS670072,SRA177126,GEO,Hubrecht Institute,2,0.37674,0.6743,0.06734,0.08523,0.92516,0.86196,0.56151,0.54745,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38080,SRR1531475,SRX665257,SRS670070,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from left to right,GSM1448814,,tissue:whole embryo|Stage:15 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from left to right,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,GSM1448814,GSM1448814: 15 somite stage  secti1d from left to right; Danio rerio; RNA Seq,GSM1448814,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448814,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_15ss_LR_R2.fastq.gz dr_15ss_LR_R1.fastq.gz,fastq fastq,2077803342.0,20370621.0,GSM1448814 r1,0:51 1:51,A:487276259;C:320933398;G:342175116;T:925418636;N:1999933,51,51,,,487276259,320933398,342175116,925418636,1999933,SRX665257,SRS670070,SRA177126,GEO,Hubrecht Institute,2,0.04544,0.77533,0.03741,0.15439,0.98435,0.77662,0.56397,0.57005,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38081,SRR1531476,SRX665257,SRS670070,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from left to right,GSM1448814,,tissue:whole embryo|Stage:15 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from left to right,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,GSM1448814,GSM1448814: 15 somite stage  secti1d from left to right; Danio rerio; RNA Seq,GSM1448814,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448814,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_15ss_LR_R1.fastq.gz miseq_dr_15ss_LR_R2.fastq.gz,fastq fastq,648479770.0,1294232.0,GSM1448814 r2,0:251 1:250.05,A:208271519;C:133135452;G:114142609;T:192930139;N:51,251,250,,,208271519,133135452,114142609,192930139,51,SRX665257,SRS670070,SRA177126,GEO,Hubrecht Institute,2,0.34992,0.64011,0.08713,0.16967,0.92103,0.83853,0.54292,0.52547,251,250,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38082,SRR1531473,SRX665256,SRS670071,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from dorsal to ventral end,GSM1448813,,tissue:whole embryo|Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from dorsal to ventral end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,GSM1448813,GSM1448813: 15 somite stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq,GSM1448813,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448813,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_15ss_DV_R1.fastq.gz dr_15ss_DV_R2.fastq.gz,fastq fastq,2516804610.0,24674555.0,GSM1448813 r1,0:51 1:51,A:579818006;C:406550753;G:379205422;T:1129932140;N:21298289,51,51,,,579818006,406550753,379205422,1129932140,21298289,SRX665256,SRS670071,SRA177126,GEO,Hubrecht Institute,2,0.04189,0.74891,0.03368,0.12625,0.98695,0.78423,0.46823,0.53429,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38083,SRR1531474,SRX665256,SRS670071,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from dorsal to ventral end,GSM1448813,,tissue:whole embryo|Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from dorsal to ventral end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,GSM1448813,GSM1448813: 15 somite stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq,GSM1448813,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448813,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_15ss_DV_R1.fastq.gz miseq_dr_15ss_DV_R2.fastq.gz,fastq fastq,1831352383.0,3654695.0,GSM1448813 r2,0:251 1:250.10,A:593055798;C:392880040;G:312965357;T:532451118;N:70,251,250,,,593055798,392880040,312965357,532451118,70,SRX665256,SRS670071,SRA177126,GEO,Hubrecht Institute,2,0.27976,0.58087,0.05423,0.08127,0.93943,0.88868,0.51246,0.50653,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38084,SRR1531471,SRX665255,SRS670069,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from ventral to dorsal end,GSM1448812,,tissue:whole embryo|Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from ventral to dorsal end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448812,GSM1448812: 15 somite stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq,GSM1448812,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448812,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_15ss_VD_R1.fastq.gz dr_15ss_VD_R2.fastq.gz,fastq fastq,1673808678.0,16409889.0,GSM1448812 r1,0:51 1:51,A:397744759;C:269067687;G:250815180;T:740808813;N:15372239,51,51,,,397744759,269067687,250815180,740808813,15372239,SRX665255,SRS670069,SRA177126,GEO,Hubrecht Institute,2,0.05917,0.69313,0.0499,0.19364,0.98364,0.78232,0.54626,0.5434,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38085,SRR1531472,SRX665255,SRS670069,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from ventral to dorsal end,GSM1448812,,tissue:whole embryo|Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from ventral to dorsal end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448812,GSM1448812: 15 somite stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq,GSM1448812,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448812,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_15ss_VD_R2.fastq.gz miseq_dr_15ss_VD_R1.fastq.gz,fastq fastq,587520609.0,1172567.0,GSM1448812 r2,0:251 1:250.06,A:194391951;C:123162952;G:98682047;T:171283648;N:11,251,250,,,194391951,123162952,98682047,171283648,11,SRX665255,SRS670069,SRA177126,GEO,Hubrecht Institute,2,0.25906,0.51091,0.10052,0.13544,0.94274,0.90015,0.54255,0.53365,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38086,SRR1531470,SRX665254,SRS670068,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from posterior to anterior end,GSM1448811,,tissue:whole embryo|Stage:15 somites|sectioning direction:posterior anterior|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from posterior to anterior end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:posterior anterior|section thickness:18 µm|embedding strategy:intact embryo,GSM1448811,GSM1448811: 15 somite stage  secti1d from posterior to anterior end; Danio rerio; RNA Seq,GSM1448811,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448811,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_15ss_PA_R2.fastq.gz dr_15ss_PA_R1.fastq.gz,fastq fastq,2483143794.0,24344547.0,GSM1448811 r1,0:51 1:51,A:563038776;C:400378151;G:372280878;T:1126633332;N:20812657,51,51,,,563038776,400378151,372280878,1126633332,20812657,SRX665254,SRS670068,SRA177126,GEO,Hubrecht Institute,2,0.04278,0.78001,0.03367,0.11539,0.98727,0.77865,0.49734,0.53041,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38087,SRR1531469,SRX665253,SRS670067,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from anterior to posterior end,GSM1448810,,tissue:whole embryo|Stage:15 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from anterior to posterior end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,GSM1448810,GSM1448810: 15 somite stage  secti1d from anterior to posterior end; Danio rerio; RNA Seq,GSM1448810,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448810,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_15ss_AP_R2.fastq.gz dr_15ss_AP_R1.fastq.gz,fastq fastq,3436281570.0,33689035.0,GSM1448810 r1,0:51 1:51,A:794842891;C:552474558;G:514289189;T:1545720661;N:28954271,51,51,,,794842891,552474558,514289189,1545720661,28954271,SRX665253,SRS670067,SRA177126,GEO,Hubrecht Institute,2,0.04616,0.72787,0.03714,0.11902,0.98636,0.78372,0.50428,0.54252,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38088,SRR1531468,SRX665252,SRS670066,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from right to left,GSM1448809,,tissue:whole embryo|Stage:10 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from right to left,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,GSM1448809,GSM1448809: 10 somite stage  secti1d from right to left; Danio rerio; RNA Seq,GSM1448809,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448809,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_10ss_RL_R2.fastq.gz dr_10ss_RL_R1.fastq.gz,fastq fastq,2058025848.0,20176724.0,GSM1448809 r1,0:51 1:51,A:466388690;C:327195544;G:324646168;T:921984274;N:17811172,51,51,,,466388690,327195544,324646168,921984274,17811172,SRX665252,SRS670066,SRA177126,GEO,Hubrecht Institute,2,0.03352,0.82842,0.02775,0.10176,0.99019,0.7878,0.56827,0.53664,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38089,SRR1531467,SRX665251,SRS670065,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from left to right,GSM1448808,,tissue:whole embryo|Stage:10 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from left to right,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,GSM1448808,GSM1448808: 10 somite stage  secti1d from left to right; Danio rerio; RNA Seq,GSM1448808,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448808,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_10ss_LR_R1.fastq.gz dr_10ss_LR_R2.fastq.gz,fastq fastq,2372600886.0,23260793.0,GSM1448808 r1,0:51 1:51,A:539978604;C:369014393;G:373430985;T:1069557826;N:20619078,51,51,,,539978604,369014393,373430985,1069557826,20619078,SRX665251,SRS670065,SRA177126,GEO,Hubrecht Institute,2,0.04947,0.82594,0.04114,0.11817,0.98703,0.77727,0.5181,0.46105,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38090,SRR1531465,SRX665250,SRS670064,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from dorsal to ventral end,GSM1448807,,tissue:whole embryo|Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from dorsal to ventral end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,GSM1448807,GSM1448807: 10 somite stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq,GSM1448807,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448807,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_10ss_DV_R1.fastq.gz dr_10ss_DV_R2.fastq.gz,fastq fastq,4808137200.0,47138600.0,GSM1448807 r1,0:51 1:51,A:1069537756;C:773357615;G:788490520;T:2131916220;N:44835089,51,51,,,1069537756,773357615,788490520,2131916220,44835089,SRX665250,SRS670064,SRA177126,GEO,Hubrecht Institute,2,0.05336,0.7348,0.04376,0.11098,0.98311,0.78829,0.55869,0.5169,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38091,SRR1531466,SRX665250,SRS670064,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from dorsal to ventral end,GSM1448807,,tissue:whole embryo|Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from dorsal to ventral end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,GSM1448807,GSM1448807: 10 somite stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq,GSM1448807,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448807,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_10ss_DV_R1.fastq.gz miseq_dr_10ss_DV_R2.fastq.gz,fastq fastq,981031778.0,1957880.0,GSM1448807 r2,0:251 1:250.07,A:318017696;C:204637111;G:170546834;T:287830124;N:13,251,250,,,318017696,204637111,170546834,287830124,13,SRX665250,SRS670064,SRA177126,GEO,Hubrecht Institute,2,0.28421,0.5957,0.04748,0.07361,0.93917,0.88298,0.53618,0.53493,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38092,SRR1531463,SRX665249,SRS670063,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from ventral to dorsal end,GSM1448806,,tissue:whole embryo|Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from ventral to dorsal end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448806,GSM1448806: 10 somite stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq,GSM1448806,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448806,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_10ss_VD_R1.fastq.gz dr_10ss_VD_R2.fastq.gz,fastq fastq,4042242048.0,39629824.0,GSM1448806 r1,0:51 1:51,A:880941046;C:636899286;G:642176352;T:1845085169;N:37140195,51,51,,,880941046,636899286,642176352,1845085169,37140195,SRX665249,SRS670063,SRA177126,GEO,Hubrecht Institute,2,0.04898,0.80518,0.04234,0.10309,0.99044,0.78437,0.4974,0.53264,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38093,SRR1531464,SRX665249,SRS670063,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from ventral to dorsal end,GSM1448806,,tissue:whole embryo|Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from ventral to dorsal end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448806,GSM1448806: 10 somite stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq,GSM1448806,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448806,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_10ss_VD_R1.fastq.gz miseq_dr_10ss_VD_R2.fastq.gz,fastq fastq,738071470.0,1473056.0,GSM1448806 r2,0:251 1:250.05,A:241662059;C:148514183;G:127467910;T:220427298;N:20,251,250,,,241662059,148514183,127467910,220427298,20,SRX665249,SRS670063,SRA177126,GEO,Hubrecht Institute,2,0.33554,0.65168,0.04798,0.07375,0.93334,0.87121,0.53425,0.51721,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38094,SRR1531461,SRX665248,SRS670062,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from posterior to anterior end,GSM1448805,,tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from posterior to anterior end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,GSM1448805,GSM1448805: 10 somite stage  secti1d from posterior to anterior end; Danio rerio; RNA Seq,GSM1448805,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448805,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_10ss_PA_R1.fastq.gz dr_10ss_PA_R2.fastq.gz,fastq fastq,4759203720.0,46658860.0,GSM1448805 r1,0:51 1:51,A:1044025561;C:745846492;G:761494052;T:2164007108;N:43830507,51,51,,,1044025561,745846492,761494052,2164007108,43830507,SRX665248,SRS670062,SRA177126,GEO,Hubrecht Institute,2,0.04594,0.81204,0.0388,0.10992,0.98938,0.78244,0.51272,0.52639,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38095,SRR1531462,SRX665248,SRS670062,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from posterior to anterior end,GSM1448805,,tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from posterior to anterior end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,GSM1448805,GSM1448805: 10 somite stage  secti1d from posterior to anterior end; Danio rerio; RNA Seq,GSM1448805,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448805,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_10ss_PA_R2.fastq.gz miseq_dr_10ss_PA_R1.fastq.gz,fastq fastq,923948352.0,1843960.0,GSM1448805 r2,0:251 1:250.07,A:301981474;C:189568545;G:157916393;T:274481921;N:19,251,250,,,301981474,189568545,157916393,274481921,19,SRX665248,SRS670062,SRA177126,GEO,Hubrecht Institute,2,0.33803,0.65569,0.05131,0.07917,0.93419,0.87355,0.4399,0.52526,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38096,SRR1531460,SRX665247,SRS670061,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from anterior to posterior end  replicate,GSM1448804,,tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from anterior to posterior end  replicate,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,GSM1448804,GSM1448804: 10 somite stage  secti1d from anterior to posterior end  replicate; Danio rerio; RNA Seq,GSM1448804,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448804,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_10ss_AP2_R1.fastq.gz dr_10ss_AP2_R2.fastq.gz,fastq fastq,2096761878.0,20556489.0,GSM1448804 r1,0:51 1:51,A:486131317;C:330426143;G:323887100;T:938024368;N:18292950,51,51,,,486131317,330426143,323887100,938024368,18292950,SRX665247,SRS670061,SRA177126,GEO,Hubrecht Institute,2,0.0484,0.78914,0.0396,0.12303,0.9866,0.78234,0.53395,0.53422,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38097,SRR1531458,SRX665246,SRS670060,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from anterior to posterior end,GSM1448803,,tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from anterior to posterior end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,GSM1448803,GSM1448803: 10 somite stage  secti1d from anterior to posterior end; Danio rerio; RNA Seq,GSM1448803,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448803,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_10ss_AP_R2.fastq.gz dr_10ss_AP_R1.fastq.gz,fastq fastq,3873169500.0,37972250.0,GSM1448803 r1,0:51 1:51,A:844434990;C:614503150;G:615061181;T:1763736099;N:35434080,51,51,,,844434990,614503150,615061181,1763736099,35434080,SRX665246,SRS670060,SRA177126,GEO,Hubrecht Institute,2,0.0354,0.81065,0.02893,0.12263,0.98944,0.77386,0.52631,0.52007,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38098,SRR1531459,SRX665246,SRS670060,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from anterior to posterior end,GSM1448803,,tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from anterior to posterior end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,GSM1448803,GSM1448803: 10 somite stage  secti1d from anterior to posterior end; Danio rerio; RNA Seq,GSM1448803,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448803,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_10ss_AP_R1.fastq.gz miseq_dr_10ss_AP_R2.fastq.gz,fastq fastq,496084013.0,990096.0,GSM1448803 r2,0:251 1:250.05,A:161790706;C:99237964;G:85634725;T:149420610;N:8,251,250,,,161790706,99237964,85634725,149420610,8,SRX665246,SRS670060,SRA177126,GEO,Hubrecht Institute,2,0.35483,0.66804,0.06659,0.09269,0.92699,0.86113,0.53381,0.51797,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38099,SRR1531457,SRX665245,SRS670059,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from dorsal to ventral end  replicate,GSM1448802,,tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from dorsal to ventral end  replicate,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,GSM1448802,GSM1448802: shield stage  secti1d from dorsal to ventral end  replicate; Danio rerio; RNA Seq,GSM1448802,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448802,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_DV2_R2.fastq.gz dr_shield_DV2_R1.fastq.gz,fastq fastq,2735350014.0,26817157.0,GSM1448802 r1,0:51 1:51,A:650077339;C:412458828;G:411687121;T:1237686190;N:23440536,51,51,,,650077339,412458828,411687121,1237686190,23440536,SRX665245,SRS670059,SRA177126,GEO,Hubrecht Institute,2,0.02556,0.75175,0.01912,0.10697,0.99076,0.79819,0.54093,0.55229,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38100,SRR1531455,SRX665244,SRS670058,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from dorsal to ventral end,GSM1448801,,tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from dorsal to ventral end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,GSM1448801,GSM1448801: shield stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq,GSM1448801,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448801,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_DV_R1.fastq.gz dr_shield_DV_R2.fastq.gz,fastq fastq,1605318738.0,15738419.0,GSM1448801 r1,0:51 1:51,A:361176217;C:248822696;G:253372108;T:726629351;N:15318366,51,51,,,361176217,248822696,253372108,726629351,15318366,SRX665244,SRS670058,SRA177126,GEO,Hubrecht Institute,2,0.02633,0.68496,0.02344,0.10104,0.99638,0.80006,0.46031,0.57655,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38101,SRR1531456,SRX665244,SRS670058,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from dorsal to ventral end,GSM1448801,,tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from dorsal to ventral end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,GSM1448801,GSM1448801: shield stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq,GSM1448801,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448801,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_shield_DV_R1.fastq.gz miseq_dr_shield_DV_R2.fastq.gz,fastq fastq,114907294.0,229320.0,GSM1448801 r2,0:251 1:250.08,A:37813553;C:24168661;G:19441624;T:33483456;N:0,251,250,,,37813553,24168661,19441624,33483456,0,SRX665244,SRS670058,SRA177126,GEO,Hubrecht Institute,2,0.26022,0.46204,0.03083,0.05933,0.94627,0.89301,0.56728,0.55478,251,250,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38102,SRR1531453,SRX665243,SRS670056,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from ventral to dorsal end,GSM1448800,,tissue:whole embryo|Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from ventral to dorsal end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448800,GSM1448800: shield stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq,GSM1448800,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448800,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_VD_R1.fastq.gz dr_shield_VD_R2.fastq.gz,fastq fastq,1840839492.0,18047446.0,GSM1448800 r1,0:51 1:51,A:421253850;C:292045914;G:295175858;T:814744774;N:17619096,51,51,,,421253850,292045914,295175858,814744774,17619096,SRX665243,SRS670056,SRA177126,GEO,Hubrecht Institute,2,0.01815,0.6287,0.01468,0.09567,0.99452,0.80975,0.5259,0.58926,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38103,SRR1531454,SRX665243,SRS670056,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from ventral to dorsal end,GSM1448800,,tissue:whole embryo|Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from ventral to dorsal end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448800,GSM1448800: shield stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq,GSM1448800,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448800,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_shield_VD_R2.fastq.gz miseq_dr_shield_VD_R1.fastq.gz,fastq fastq,158531701.0,316379.0,GSM1448800 r2,,,,,,,,,,,,SRX665243,SRS670056,SRA177126,GEO,Hubrecht Institute,2,0.06803,0.1733,0.00916,0.026,0.94085,0.88899,0.58254,0.5723,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38104,SRR1531451,SRX665242,SRS670055,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from right to left,GSM1448799,,tissue:whole embryo|Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from right to left,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,GSM1448799,GSM1448799: shield stage  secti1d from right to left; Danio rerio; RNA Seq,GSM1448799,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448799,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_RL_R1.fastq.gz dr_shield_RL_R2.fastq.gz,fastq fastq,2003076918.0,19638009.0,GSM1448799 r1,0:51 1:51,A:457537608;C:308292947;G:312973612;T:905317961;N:18954790,51,51,,,457537608,308292947,312973612,905317961,18954790,SRX665242,SRS670055,SRA177126,GEO,Hubrecht Institute,2,0.02111,0.7573,0.01656,0.11316,0.99364,0.8005,0.4501,0.59142,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38105,SRR1531452,SRX665242,SRS670055,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from right to left,GSM1448799,,tissue:whole embryo|Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from right to left,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,GSM1448799,GSM1448799: shield stage  secti1d from right to left; Danio rerio; RNA Seq,GSM1448799,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448799,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_shield_RL_R1.fastq.gz miseq_dr_shield_RL_R2.fastq.gz,fastq fastq,154180181.0,307695.0,GSM1448799 r2,0:251 1:250.08,A:50801230;C:32293099;G:25917988;T:45167860;N:4,251,250,,,50801230,32293099,25917988,45167860,4,SRX665242,SRS670055,SRA177126,GEO,Hubrecht Institute,2,0.31553,0.64085,0.03613,0.06829,0.94101,0.8938,0.60272,0.58117,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38106,SRR1531449,SRX665241,SRS670053,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from left to right,GSM1448798,,tissue:whole embryo|Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from left to right,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,GSM1448798,GSM1448798: shield stage  secti1d from left to right; Danio rerio; RNA Seq,GSM1448798,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448798,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_LR_R1.fastq.gz dr_shield_LR_R2.fastq.gz,fastq fastq,1755442542.0,17210221.0,GSM1448798 r1,0:51 1:51,A:401133098;C:265688355;G:264899378;T:807011867;N:16709844,51,51,,,401133098,265688355,264899378,807011867,16709844,SRX665241,SRS670053,SRA177126,GEO,Hubrecht Institute,2,0.02829,0.71918,0.02455,0.14486,0.99484,0.79866,0.50383,0.57925,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38107,SRR1531450,SRX665241,SRS670053,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from left to right,GSM1448798,,tissue:whole embryo|Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from left to right,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,GSM1448798,GSM1448798: shield stage  secti1d from left to right; Danio rerio; RNA Seq,GSM1448798,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448798,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_shield_LR_R1.fastq.gz miseq_dr_shield_LR_R2.fastq.gz,fastq fastq,139755993.0,278913.0,GSM1448798 r2,0:251 1:250.07,A:46536591;C:28346077;G:23036783;T:41836538;N:4,251,250,,,46536591,28346077,23036783,41836538,4,SRX665241,SRS670053,SRA177126,GEO,Hubrecht Institute,2,0.27443,0.57858,0.06346,0.09954,0.94194,0.89522,0.55896,0.56169,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38108,SRR1531448,SRX665240,SRS670054,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from vegetal to animal pole  replicate,GSM1448797,,tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from vegetal to animal pole  replicate,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448797,GSM1448797: shield stage  secti1d from vegetal to animal pole  replicate; Danio rerio; RNA Seq,GSM1448797,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448797,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_VA2_R1.fastq.gz dr_shield_VA2_R2.fastq.gz,fastq fastq,1962884532.0,19243966.0,GSM1448797 r1,0:51 1:51,A:449529690;C:292065368;G:287973067;T:916330652;N:16985755,51,51,,,449529690,292065368,287973067,916330652,16985755,SRX665240,SRS670054,SRA177126,GEO,Hubrecht Institute,2,0.04512,0.77455,0.03997,0.11233,0.99293,0.78488,0.50931,0.5171,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38109,SRR1531446,SRX665239,SRS670057,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from vegetal to animal pole,GSM1448796,,tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from vegetal to animal pole,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448796,GSM1448796: shield stage  secti1d from vegetal to animal pole; Danio rerio; RNA Seq,GSM1448796,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448796,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_VA_R2.fastq.gz dr_shield_VA_R1.fastq.gz,fastq fastq,2367839934.0,23214117.0,GSM1448796 r1,0:51 1:51,A:544061124;C:369321045;G:383489434;T:1047897582;N:23070749,51,51,,,544061124,369321045,383489434,1047897582,23070749,SRX665239,SRS670057,SRA177126,GEO,Hubrecht Institute,2,0.02284,0.57831,0.0199,0.08251,0.99579,0.81653,0.4451,0.5792,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38110,SRR1531447,SRX665239,SRS670057,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from vegetal to animal pole,GSM1448796,,tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from vegetal to animal pole,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448796,GSM1448796: shield stage  secti1d from vegetal to animal pole; Danio rerio; RNA Seq,GSM1448796,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448796,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_shield_VA_R1.fastq.gz miseq_dr_shield_VA_R2.fastq.gz,fastq fastq,139677889.0,278764.0,GSM1448796 r2,0:251 1:250.06,A:45877333;C:29821713;G:24032460;T:39946380;N:3,251,250,,,45877333,29821713,24032460,39946380,3,SRX665239,SRS670057,SRA177126,GEO,Hubrecht Institute,2,0.21444,0.33364,0.02489,0.04529,0.95156,0.901,0.56549,0.55749,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38111,SRR1531444,SRX665238,SRS670052,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from animal to vegetal pole,GSM1448795,,tissue:whole embryo|Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from animal to vegetal pole,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448795,GSM1448795: shield stage  secti1d from animal to vegetal pole; Danio rerio; RNA Seq,GSM1448795,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448795,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_AV_R1.fastq.gz dr_shield_AV_R2.fastq.gz,fastq fastq,2059615110.0,20192305.0,GSM1448795 r1,0:51 1:51,A:487942041;C:328047311;G:336282927;T:886836259;N:20506572,51,51,,,487942041,328047311,336282927,886836259,20506572,SRX665238,SRS670052,SRA177126,GEO,Hubrecht Institute,2,0.01633,0.50842,0.0136,0.07269,0.99541,0.82183,0.51242,0.59281,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38112,SRR1531445,SRX665238,SRS670052,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from animal to vegetal pole,GSM1448795,,tissue:whole embryo|Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from animal to vegetal pole,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448795,GSM1448795: shield stage  secti1d from animal to vegetal pole; Danio rerio; RNA Seq,GSM1448795,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448795,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_shield_AV_R1.fastq.gz miseq_dr_shield_AV_R2.fastq.gz,fastq fastq,176530873.0,352271.0,GSM1448795 r2,0:251 1:250.12,A:57029265;C:38838035;G:30065677;T:50597891;N:5,251,250,,,57029265,38838035,30065677,50597891,5,SRX665238,SRS670052,SRA177126,GEO,Hubrecht Institute,2,0.20318,0.26844,0.02342,0.03751,0.95499,0.9069,0.4325,0.57102,251,251,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
39741,SRR2089842,SRX1085056,SRS981139,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD + spt cMO replicate 5,GSM1812032,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,cFD + spt cMO replicate 5,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,GSM1812032,GSM1812032: cFD + spt cMO replicate 5; Danio rerio; RNA Seq,GSM1812032,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812032,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cMO_5_1.bz2 cMO_5_2.bz2,fastq fastq,2590806954.0,12825777.0,GSM1812032 r1,0:101 1:101,A:729527639;C:388090931;G:473627524;T:996733909;N:2826951,101,101,,,729527639,388090931,473627524,996733909,2826951,SRX1085056,SRS981139,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.34765,0.81821,0.09574,0.11092,0.96846,0.84273,0.56486,0.60514,101,101,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
39742,SRR2089841,SRX1085055,SRS981140,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD + spt cMO replicate 4,GSM1812031,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,cFD + spt cMO replicate 4,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,GSM1812031,GSM1812031: cFD + spt cMO replicate 4; Danio rerio; RNA Seq,GSM1812031,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812031,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cMO_4_2.bz2 cMO_4_1.bz2,fastq fastq,4576986902.0,22658351.0,GSM1812031 r1,0:101 1:101,A:1236262881;C:739179623;G:837030962;T:1759535468;N:4977968,101,101,,,1236262881,739179623,837030962,1759535468,4977968,SRX1085055,SRS981140,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.4938,0.83831,0.1798,0.13149,0.96593,0.84766,0.57231,0.63621,101,101,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
39743,SRR2089840,SRX1085054,SRS981143,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD + spt cMO replicate 3,GSM1812030,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,cFD + spt cMO replicate 3,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,GSM1812030,GSM1812030: cFD + spt cMO replicate 3; Danio rerio; RNA Seq,GSM1812030,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812030,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cMO_3_1.bz2 cMO_3_2.bz2,fastq fastq,2769659976.0,13711188.0,GSM1812030 r1,0:101 1:101,A:801844710;C:425581810;G:477170945;T:1062200254;N:2862257,101,101,,,801844710,425581810,477170945,1062200254,2862257,SRX1085054,SRS981143,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.36913,0.82247,0.20581,0.12151,0.97656,0.84589,0.57375,0.61151,101,101,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
39744,SRR2089839,SRX1085053,SRS981142,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD + spt cMO replicate 2,GSM1812029,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,cFD + spt cMO replicate 2,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,GSM1812029,GSM1812029: cFD + spt cMO replicate 2; Danio rerio; RNA Seq,GSM1812029,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812029,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cMO_2_1.bz2 cMO_2_2.bz2,fastq fastq,2482029348.0,12287274.0,GSM1812029 r1,0:101 1:101,A:675627490;C:417393063;G:437628865;T:948867297;N:2512633,101,101,,,675627490,417393063,437628865,948867297,2512633,SRX1085053,SRS981142,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.49124,0.82814,0.19593,0.12778,0.96694,0.84814,0.61289,0.65915,101,101,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
39745,SRR2089838,SRX1085052,SRS981141,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD + spt cMO replicate 1,GSM1812028,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,cFD + spt cMO replicate 1,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,GSM1812028,GSM1812028: cFD + spt cMO replicate 1; Danio rerio; RNA Seq,GSM1812028,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812028,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cMO_1_1.bz2 cMO_1_2.bz2,fastq fastq,7585699334.0,37552967.0,GSM1812028 r1,0:101 1:101,A:1977695961;C:1274396713;G:1452711269;T:2871964961;N:8930430,101,101,,,1977695961,1274396713,1452711269,2871964961,8930430,SRX1085052,SRS981141,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.48942,0.85323,0.16329,0.18148,0.97236,0.8565,0.59311,0.63618,101,101,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
39746,SRR2089837,SRX1085051,SRS981144,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD only replicate 5,GSM1812027,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,cFD only replicate 5,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,GSM1812027,GSM1812027: cFD only replicate 5; Danio rerio; RNA Seq,GSM1812027,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812027,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cntrl_5_1.bz2 cntrl_5_2.bz2,fastq fastq,4762488754.0,23576677.0,GSM1812027 r1,0:101 1:101,A:1380401515;C:716191196;G:808857049;T:1851642812;N:5396182,101,101,,,1380401515,716191196,808857049,1851642812,5396182,SRX1085051,SRS981144,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.4168,0.81605,0.16291,0.11435,0.97185,0.84354,0.6892,0.61855,101,101,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
39747,SRR2089836,SRX1085050,SRS981145,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD only replicate 4,GSM1812026,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,cFD only replicate 4,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,GSM1812026,GSM1812026: cFD only replicate 4; Danio rerio; RNA Seq,GSM1812026,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812026,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cntrl_4_1.bz2 cntrl_4_2.bz2,fastq fastq,3719006042.0,18410921.0,GSM1812026 r1,0:101 1:101,A:1038933535;C:615185731;G:647242496;T:1413253009;N:4391271,101,101,,,1038933535,615185731,647242496,1413253009,4391271,SRX1085050,SRS981145,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.46956,0.82686,0.12167,0.11363,0.97025,0.85074,0.58699,0.63586,101,101,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
39748,SRR2089835,SRX1085049,SRS981146,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD only replicate 3,GSM1812025,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,cFD only replicate 3,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,GSM1812025,GSM1812025: cFD only replicate 3; Danio rerio; RNA Seq,GSM1812025,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812025,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cntrl_3_2.bz2 cntrl_3_1.bz2,fastq fastq,2513713250.0,12444125.0,GSM1812025 r1,0:101 1:101,A:709549704;C:390305955;G:451783096;T:959236114;N:2838381,101,101,,,709549704,390305955,451783096,959236114,2838381,SRX1085049,SRS981146,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.41236,0.81226,0.11339,0.11567,0.97051,0.85305,0.60801,0.4295,101,101,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
39749,SRR2089834,SRX1085048,SRS981148,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD only replicate 2,GSM1812024,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,cFD only replicate 2,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,GSM1812024,GSM1812024: cFD only replicate 2; Danio rerio; RNA Seq,GSM1812024,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812024,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cntrl_2_1.bz2 cntrl_2_2.bz2,fastq fastq,6157457728.0,30482464.0,GSM1812024 r1,0:101 1:101,A:1679764131;C:1000368713;G:1086099790;T:2384200862;N:7024232,101,101,,,1679764131,1000368713,1086099790,2384200862,7024232,SRX1085048,SRS981148,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.47785,0.82086,0.20529,0.14023,0.97226,0.85232,0.65332,0.66262,101,101,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
39750,SRR2089833,SRX1085047,SRS981147,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD only replicate 1,GSM1812023,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,cFD only replicate 1,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,GSM1812023,GSM1812023: cFD only replicate 1; Danio rerio; RNA Seq,GSM1812023,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812023,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cntrl_1_1.bz2 cntrl_1_2.bz2,fastq fastq,4291177304.0,21243452.0,GSM1812023 r1,0:101 1:101,A:1182202535;C:708780301;G:753724632;T:1641921837;N:4547999,101,101,,,1182202535,708780301,753724632,1641921837,4547999,SRX1085047,SRS981147,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.45088,0.8425,0.11253,0.11641,0.97835,0.84778,0.46728,0.64503,101,101,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
40164,SRR2921973,SRX1432516,SRS1163508,SRP066192,PRJNA302179,Genome–wide transcriptional profiling with spatial resolution identifies Bone Morphogenetic Protein signaling as essential regulator of zebrafish cardiomyocyte regeneration.,GSE74652,Transcriptome Analysis,In contrast to mammals  zebrafish regenerate heart injuries via proliferation of cardiomyocytes located at the wound border. Here  we show that tomo seq can be used to identify whole genome transcriptional profiles of the injury zone  the border zone and the healthy myocardium. Interestingly  the border zone is characterized by the re expression of embryonic cardiac genes that are also activated post myocardial infarction in mouse and human  including targets of Bone Morphogenetic Protein BMP signaling. Endogenous BMP signaling has been reported to be detrimental to mammalian cardiac repair. In contrast  we find that genetic or chemical inhibition of BMP signaling in zebrafish reduces cardiomyocyte dedifferentiation and proliferation  ultimately compromising myocardial regeneration  while bmp2b overexpression is sufficient to enhance it. Our results provide a resource for further studies on the molecular regulation of cardiac regeneration and reveal intriguing differential cellular responses of cardiomyocytes to a conserved signaling pathway in regenerative versus non regenerative hearts. Overall design: To generate spatially resolved RNA seq data for injured zebrafish hearts 3 and 7 xxx post injury  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina NextSeq  using 75bp paired end sequencing.,,pubmed:26748692,,zebrafish heart WT 7dpi #1,GSM1924888,,source name:cryoinjured ventricle of the heart|tissue:adult heart|sectioning direction:injury area   uninjured  remote myocardium|sectioning thickness:12 µm|embedding strategy:extracted heart at 7 days post cryoinjury,zebrafish heart WT 7dpi #1,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,cryoinjured ventricle of the heart,Unfixed ventricle was embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see: Junker et al.  2014  Cell,,tissue:adult heart|sectioning direction:injury area   uninjured  remote myocardium|sectioning thickness:12 µm|embedding strategy:extracted heart at 7 days post cryoinjury,GSM1924888,GSM1924888: zebrafish heart WT 7dpi #1; Danio rerio; RNA Seq,GSM1924888,,1,RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see: Junker et al.  2014  Cell,GEO Accession:GSM1924888,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP066192,,,FKHEART7_R1.fastq.gz FKHEART7_R2.fastq.gz,fastq fastq,3128649900.0,20745605.0,GSM1924888 r1,0:75.43 1:75.38,A:1025473014;C:388501715;G:410501025;T:1304153289;N:20857,75,75,,,1025473014,388501715,410501025,1304153289,20857,SRX1432516,SRS1163508,SRA311639,GEO,"Jeroen Bakkers, Hubrecht Institute",2,0.31194,0.62458,0.26968,0.18109,0.99308,0.89258,0.54708,0.5286,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,celseq,,Netherlands,2015-11-03,Adult,Adult,Heart,Cardiovascular System
40165,SRR2921972,SRX1432515,SRS1163510,SRP066192,PRJNA302179,Genome–wide transcriptional profiling with spatial resolution identifies Bone Morphogenetic Protein signaling as essential regulator of zebrafish cardiomyocyte regeneration.,GSE74652,Transcriptome Analysis,In contrast to mammals  zebrafish regenerate heart injuries via proliferation of cardiomyocytes located at the wound border. Here  we show that tomo seq can be used to identify whole genome transcriptional profiles of the injury zone  the border zone and the healthy myocardium. Interestingly  the border zone is characterized by the re expression of embryonic cardiac genes that are also activated post myocardial infarction in mouse and human  including targets of Bone Morphogenetic Protein BMP signaling. Endogenous BMP signaling has been reported to be detrimental to mammalian cardiac repair. In contrast  we find that genetic or chemical inhibition of BMP signaling in zebrafish reduces cardiomyocyte dedifferentiation and proliferation  ultimately compromising myocardial regeneration  while bmp2b overexpression is sufficient to enhance it. Our results provide a resource for further studies on the molecular regulation of cardiac regeneration and reveal intriguing differential cellular responses of cardiomyocytes to a conserved signaling pathway in regenerative versus non regenerative hearts. Overall design: To generate spatially resolved RNA seq data for injured zebrafish hearts 3 and 7 xxx post injury  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina NextSeq  using 75bp paired end sequencing.,,pubmed:26748692,,zebrafish heart WT 3dpi #1,GSM1924887,,source name:cryoinjured ventricle of the heart|tissue:adult heart|sectioning direction:injury area   uninjured  remote myocardium|sectioning thickness:12 µm|embedding strategy:extracted heart at 3 days post cryoinjury,zebrafish heart WT 3dpi #1,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,cryoinjured ventricle of the heart,Unfixed ventricle was embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see: Junker et al.  2014  Cell,,tissue:adult heart|sectioning direction:injury area   uninjured  remote myocardium|sectioning thickness:12 µm|embedding strategy:extracted heart at 3 days post cryoinjury,GSM1924887,GSM1924887: zebrafish heart WT 3dpi #1; Danio rerio; RNA Seq,GSM1924887,,1,RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see: Junker et al.  2014  Cell,GEO Accession:GSM1924887,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP066192,,,FKHEART3_R1.fastq.gz FKHEART3_R2.fastq.gz,fastq fastq,784558404.0,5209213.0,GSM1924887 r1,0:75.22 1:75.39,A:291009319;C:102718146;G:111606154;T:279144074;N:80711,75,75,,,291009319,102718146,111606154,279144074,80711,SRX1432515,SRS1163510,SRA311639,GEO,"Jeroen Bakkers, Hubrecht Institute",2,0.12872,0.82031,0.12623,0.08476,0.99997,0.82828,0.0,0.566,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,celseq,,Netherlands,2015-11-03,Adult,Adult,Heart,Cardiovascular System
40599,SRR3231354,SRX1637105,SRS1342922,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate4.1,GSM2090871,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090871,GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090871,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate4.1_R1_001.fastq.gz 8hpf_wt_Plate4.1_R2_001.fastq.gz,fastq fastq,2340114249.0,31038332.0,GSM2090871 r1,0:75.50 1:75.29,A:719873895;C:416010081;G:472221417;T:731461092;N:547764,75,75,,,719873895,416010081,472221417,731461092,547764,SRX1637105,SRS1342922,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",1,0.00529,,0.00355,,0.99655,,0.52173,,76,,T,,under 1.2% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40600,SRR3231355,SRX1637105,SRS1342922,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate4.1,GSM2090871,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090871,GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090871,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate4.2_R1_001.fastq.gz 8hpf_wt_Plate4.2_R2_001.fastq.gz,fastq fastq,2340187687.0,31038332.0,GSM2090871 r2,0:75.50 1:75.29,A:718375391;C:414519064;G:478873036;T:728401149;N:19047,75,75,,,718375391,414519064,478873036,728401149,19047,SRX1637105,SRS1342922,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",1,0.00524,,0.00333,,0.99634,,0.47321,,76,,T,,under 1.2% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40601,SRR3231356,SRX1637105,SRS1342922,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate4.1,GSM2090871,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090871,GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090871,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate4.3_R1_001.fastq.gz 8hpf_wt_Plate4.3_R2_001.fastq.gz,fastq fastq,2331948832.0,15464230.0,GSM2090871 r3,0:75.51 1:75.29,A:710801790;C:413559417;G:478178818;T:728790143;N:618664,75,75,,,710801790,413559417,478178818,728790143,618664,SRX1637105,SRS1342922,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00263,0.00843,0.0023,0.00555,0.99955,0.99437,0.37837,0.52459,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40602,SRR3231357,SRX1637105,SRS1342922,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate4.1,GSM2090871,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090871,GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090871,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate4_R1_001.fastq.gz 8hpf_wt_Plate4_R2_001.fastq.gz,fastq fastq,2346532249.0,15562065.0,GSM2090871 r4,0:75.50 1:75.29,A:726362504;C:417435976;G:471522192;T:731180603;N:30974,75,75,,,726362504,417435976,471522192,731180603,30974,SRX1637105,SRS1342922,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0024,0.00837,0.00209,0.00548,0.99975,0.99409,0.2,0.53439,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40603,SRR3231350,SRX1637104,SRS1342923,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate3.1,GSM2090870,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090870,GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090870,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate3.1_R2_001.fastq.gz 8hpf_wt_Plate3.1_R1_001.fastq.gz,fastq fastq,1401297283.0,9290433.0,GSM2090870 r1,0:75.49 1:75.34,A:419635887;C:271951633;G:296507210;T:413191086;N:11467,75,75,,,419635887,271951633,296507210,413191086,11467,SRX1637104,SRS1342923,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00163,0.00616,0.00116,0.00341,0.99951,0.99425,0.125,0.59722,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40604,SRR3231351,SRX1637104,SRS1342923,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate3.1,GSM2090870,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090870,GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090870,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate3.2_R1_001.fastq.gz 8hpf_wt_Plate3.2_R2_001.fastq.gz,fastq fastq,1401701707.0,9293054.0,GSM2090870 r2,0:75.50 1:75.34,A:422173594;C:272799681;G:292195265;T:414209404;N:323763,75,75,,,422173594,272799681,292195265,414209404,323763,SRX1637104,SRS1342923,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00183,0.0057,0.00134,0.00307,0.99959,0.9948,0.18965,0.59402,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40605,SRR3231352,SRX1637104,SRS1342923,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate3.1,GSM2090870,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090870,GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090870,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate3.3_R1_001.fastq.gz 8hpf_wt_Plate3.3_R2_001.fastq.gz,fastq fastq,1395747908.0,9253276.0,GSM2090870 r3,0:75.50 1:75.34,A:416176386;C:270989429;G:295563056;T:412655214;N:363823,75,75,,,416176386,270989429,295563056,412655214,363823,SRX1637104,SRS1342923,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00148,0.0058,0.00112,0.00312,0.99969,0.99476,0.16279,0.54093,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40606,SRR3231353,SRX1637104,SRS1342923,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate3.1,GSM2090870,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090870,GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090870,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate3_R1_001.fastq.gz 8hpf_wt_Plate3_R2_001.fastq.gz,fastq fastq,1407551761.0,9332199.0,GSM2090870 r4,0:75.49 1:75.34,A:425795996;C:274090898;G:292401737;T:415244521;N:18609,75,75,,,425795996,274090898,292401737,415244521,18609,SRX1637104,SRS1342923,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00196,0.00615,0.00142,0.00325,0.99926,0.99403,0.39682,0.57712,74,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40607,SRR3231346,SRX1637103,SRS1342924,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate2.1,GSM2090869,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090869,GSM2090869: 8hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090869,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate2.1_R1_001.fastq.gz 8hpf_wt_Plate2.1_R2_001.fastq.gz,fastq fastq,952595024.0,6315631.0,GSM2090869 r1,0:75.47 1:75.36,A:302137554;C:151875219;G:168962721;T:329611160;N:8370,75,75,,,302137554,151875219,168962721,329611160,8370,SRX1637103,SRS1342924,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00829,0.04086,0.00683,0.01381,0.99898,0.97133,0.21481,0.68244,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40608,SRR3231347,SRX1637103,SRS1342924,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate2.1,GSM2090869,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090869,GSM2090869: 8hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090869,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate2.2_R1_001.fastq.gz 8hpf_wt_Plate2.2_R2_001.fastq.gz,fastq fastq,946451815.0,6274940.0,GSM2090869 r2,0:75.47 1:75.36,A:302374789;C:151074230;G:165028305;T:327758585;N:215906,75,75,,,302374789,151074230,165028305,327758585,215906,SRX1637103,SRS1342924,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00869,0.03997,0.00704,0.01272,0.99888,0.97183,0.24342,0.68028,75,74,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40609,SRR3231348,SRX1637103,SRS1342924,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate2.1,GSM2090869,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090869,GSM2090869: 8hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090869,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate2.3_R2_001.fastq.gz 8hpf_wt_Plate2.3_R1_001.fastq.gz,fastq fastq,947126047.0,6279272.0,GSM2090869 r3,0:75.48 1:75.36,A:299035197;C:150983123;G:168162807;T:328697140;N:247780,75,75,,,299035197,150983123,168162807,328697140,247780,SRX1637103,SRS1342924,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00868,0.03867,0.00717,0.01319,0.99864,0.97356,0.29285,0.66677,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System