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
24838,SRR25509990,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S65_L001_I1_001.fastq.gz Kristen_10X_101620_S65_L001_R1_001.fastq.gz Kristen_10X_101620_S65_L001_R2_001.fastq.gz,fastq fastq fastq,3327423622.0,26200186.0,GSM7680082 r1,0:8 1:28 2:91,A:693698335;C:494975421;G:540414923;T:654926705;N:201542,8,28,91,,693698335,494975421,540414923,654926705,201542,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91351,,0.22865,,0.77723,,0.49805,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24839,SRR25509991,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S67_L002_I1_001.fastq.gz Kristen_10X_101620_S67_L002_R1_001.fastq.gz Kristen_10X_101620_S67_L002_R2_001.fastq.gz,fastq fastq fastq,4430975390.0,34889570.0,GSM7680082 r10,0:8 1:28 2:91,A:923557751;C:658731986;G:718325003;T:874072049;N:264081,8,28,91,,923557751,658731986,718325003,874072049,264081,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91797,,0.22868,,0.77863,,0.50737,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24840,SRR25509992,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S67_L003_I1_001.fastq.gz Kristen_10X_101620_S67_L003_R1_001.fastq.gz Kristen_10X_101620_S67_L003_R2_001.fastq.gz,fastq fastq fastq,4429223552.0,34875776.0,GSM7680082 r11,0:8 1:28 2:91,A:923277621;C:658440918;G:718036099;T:873676803;N:264175,8,28,91,,923277621,658440918,718036099,873676803,264175,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91753,,0.22978,,0.77942,,0.50977,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24841,SRR25509993,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S67_L004_I1_001.fastq.gz Kristen_10X_101620_S67_L004_R1_001.fastq.gz Kristen_10X_101620_S67_L004_R2_001.fastq.gz,fastq fastq fastq,4549656890.0,35824070.0,GSM7680082 r12,0:8 1:28 2:91,A:950423951;C:673969790;G:734760168;T:900554096;N:282365,8,28,91,,950423951,673969790,734760168,900554096,282365,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91687,,0.23323,,0.77932,,0.50984,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24842,SRR25509994,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S68_L001_I1_001.fastq.gz Kristen_10X_101620_S68_L001_R1_001.fastq.gz Kristen_10X_101620_S68_L001_R2_001.fastq.gz,fastq fastq fastq,2696456634.0,21231942.0,GSM7680082 r13,0:8 1:28 2:91,A:562209710;C:401113540;G:437836456;T:530785441;N:161575,8,28,91,,562209710,401113540,437836456,530785441,161575,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91384,,0.22885,,0.77912,,0.50672,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24843,SRR25509995,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S68_L002_I1_001.fastq.gz Kristen_10X_101620_S68_L002_R1_001.fastq.gz Kristen_10X_101620_S68_L002_R2_001.fastq.gz,fastq fastq fastq,2735162932.0,21536716.0,GSM7680082 r14,0:8 1:28 2:91,A:570169460;C:406846839;G:443964376;T:538696359;N:164122,8,28,91,,570169460,406846839,443964376,538696359,164122,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91691,,0.22998,,0.77942,,0.51035,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24844,SRR25509996,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S68_L003_I1_001.fastq.gz Kristen_10X_101620_S68_L003_R1_001.fastq.gz Kristen_10X_101620_S68_L003_R2_001.fastq.gz,fastq fastq fastq,2739703563.0,21572469.0,GSM7680082 r15,0:8 1:28 2:91,A:571283074;C:407511119;G:444574049;T:539563747;N:162690,8,28,91,,571283074,407511119,444574049,539563747,162690,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91526,,0.22747,,0.7793,,0.51387,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24845,SRR25509997,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S68_L004_I1_001.fastq.gz Kristen_10X_101620_S68_L004_R1_001.fastq.gz Kristen_10X_101620_S68_L004_R2_001.fastq.gz,fastq fastq fastq,2828960433.0,22275279.0,GSM7680082 r16,0:8 1:28 2:91,A:591166850;C:419193897;G:457332081;T:559181603;N:175958,8,28,91,,591166850,419193897,457332081,559181603,175958,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91651,,0.23126,,0.77613,,0.50223,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24846,SRR25509998,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S65_L002_I1_001.fastq.gz Kristen_10X_101620_S65_L002_R1_001.fastq.gz Kristen_10X_101620_S65_L002_R2_001.fastq.gz,fastq fastq fastq,3374189340.0,26568420.0,GSM7680082 r2,0:8 1:28 2:91,A:703424426;C:501911907;G:547786373;T:664402117;N:201397,8,28,91,,703424426,501911907,547786373,664402117,201397,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91522,,0.22812,,0.77753,,0.50208,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24847,SRR25509999,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S65_L003_I1_001.fastq.gz Kristen_10X_101620_S65_L003_R1_001.fastq.gz Kristen_10X_101620_S65_L003_R2_001.fastq.gz,fastq fastq fastq,3383217516.0,26639508.0,GSM7680082 r3,0:8 1:28 2:91,A:705514047;C:503189161;G:549089218;T:666200894;N:201908,8,28,91,,705514047,503189161,549089218,666200894,201908,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91535,,0.23036,,0.78078,,0.50202,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24848,SRR25510000,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S65_L004_I1_001.fastq.gz Kristen_10X_101620_S65_L004_R1_001.fastq.gz Kristen_10X_101620_S65_L004_R2_001.fastq.gz,fastq fastq fastq,3493154050.0,27505150.0,GSM7680082 r4,0:8 1:28 2:91,A:729910298;C:517582902;G:564926384;T:690333365;N:215701,8,28,91,,729910298,517582902,564926384,690333365,215701,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91569,,0.22913,,0.77873,,0.50186,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24849,SRR25510001,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S66_L001_I1_001.fastq.gz Kristen_10X_101620_S66_L001_R1_001.fastq.gz Kristen_10X_101620_S66_L001_R2_001.fastq.gz,fastq fastq fastq,3237456187.0,25491781.0,GSM7680082 r5,0:8 1:28 2:91,A:674885196;C:481871349;G:525642933;T:637154812;N:197781,8,28,91,,674885196,481871349,525642933,637154812,197781,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91378,,0.22852,,0.77843,,0.50985,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24850,SRR25510002,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S66_L002_I1_001.fastq.gz Kristen_10X_101620_S66_L002_R1_001.fastq.gz Kristen_10X_101620_S66_L002_R2_001.fastq.gz,fastq fastq fastq,3287789081.0,25888103.0,GSM7680082 r6,0:8 1:28 2:91,A:685408765;C:489232060;G:533550966;T:647427897;N:197685,8,28,91,,685408765,489232060,533550966,647427897,197685,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91484,,0.22872,,0.78001,,0.49909,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24851,SRR25510003,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S66_L003_I1_001.fastq.gz Kristen_10X_101620_S66_L003_R1_001.fastq.gz Kristen_10X_101620_S66_L003_R2_001.fastq.gz,fastq fastq fastq,3298207145.0,25970135.0,GSM7680082 r7,0:8 1:28 2:91,A:687621787;C:490851045;G:535230137;T:649382247;N:197069,8,28,91,,687621787,490851045,535230137,649382247,197069,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91559,,0.2268,,0.77766,,0.50935,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24852,SRR25510004,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S66_L004_I1_001.fastq.gz Kristen_10X_101620_S66_L004_R1_001.fastq.gz Kristen_10X_101620_S66_L004_R2_001.fastq.gz,fastq fastq fastq,3377888088.0,26597544.0,GSM7680082 r8,0:8 1:28 2:91,A:705624374;C:500985504;G:546306692;T:667248332;N:211602,8,28,91,,705624374,500985504,546306692,667248332,211602,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91679,,0.22965,,0.77837,,0.51495,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24853,SRR25510005,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S67_L001_I1_001.fastq.gz Kristen_10X_101620_S67_L001_R1_001.fastq.gz Kristen_10X_101620_S67_L001_R2_001.fastq.gz,fastq fastq fastq,4346114117.0,34221371.0,GSM7680082 r9,0:8 1:28 2:91,A:905838814;C:646261347;G:704993570;T:856789016;N:262014,8,28,91,,905838814,646261347,704993570,856789016,262014,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91558,,0.22834,,0.7783,,0.49972,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
28818,SRR26711836,SRX22410952,SRS19443730,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  Wnt stimulation  replicate 4,GSM7885889,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  Wnt stimulation  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885889,GSM7885889: rad21 heterozugous tailbud  Wnt stimulation  replicate 4; Danio rerio; RNA Seq,GSM7885889 r1,GSM7885889,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-8-HET_S32_L001_R2_001.fastq.gz Rad21-BIO-8-HET_S32_L001_R1_001.fastq.gz,fastq fastq,3261739218.0,21610373.0,GSM7885889 r1,0:75.52 1:75.42,A:816426262;C:810367718;G:804831968;T:829974289;N:138981,75,75,,,816426262,810367718,804831968,829974289,138981,SRX22410952,SRS19443730,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96738,0.97053,0.05473,0.05415,0.72283,0.72338,0.46691,0.46731,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28819,SRR26711837,SRX22410952,SRS19443730,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  Wnt stimulation  replicate 4,GSM7885889,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  Wnt stimulation  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885889,GSM7885889: rad21 heterozugous tailbud  Wnt stimulation  replicate 4; Danio rerio; RNA Seq,GSM7885889 r1,GSM7885889,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-8-HET_S32_L002_R2_001.fastq.gz Rad21-BIO-8-HET_S32_L002_R1_001.fastq.gz,fastq fastq,3279254436.0,21726495.0,GSM7885889 r2,0:75.52 1:75.42,A:821154343;C:814711347;G:809025779;T:834224252;N:138715,75,75,,,821154343,814711347,809025779,834224252,138715,SRX22410952,SRS19443730,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96764,0.97012,0.05449,0.05364,0.72362,0.72478,0.46065,0.44816,75,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28820,SRR26711838,SRX22410951,SRS19443729,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  Wnt stimulation  replicate 4,GSM7885888,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  Wnt stimulation  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885888,GSM7885888: rad21 homozygous tailbud  Wnt stimulation  replicate 4; Danio rerio; RNA Seq,GSM7885888 r1,GSM7885888,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-4-MUT_S31_L001_R1_001.fastq.gz Rad21-BIO-4-MUT_S31_L001_R2_001.fastq.gz,fastq fastq,3815700579.0,25275353.0,GSM7885888 r1,0:75.53 1:75.43,A:962537652;C:941667596;G:934433379;T:976947974;N:113978,75,75,,,962537652,941667596,934433379,976947974,113978,SRX22410951,SRS19443729,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96535,0.96731,0.06446,0.06372,0.71928,0.71956,0.47233,0.47166,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28821,SRR26711839,SRX22410951,SRS19443729,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  Wnt stimulation  replicate 4,GSM7885888,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  Wnt stimulation  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885888,GSM7885888: rad21 homozygous tailbud  Wnt stimulation  replicate 4; Danio rerio; RNA Seq,GSM7885888 r1,GSM7885888,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-4-MUT_S31_L002_R1_001.fastq.gz Rad21-BIO-4-MUT_S31_L002_R2_001.fastq.gz,fastq fastq,3837906036.0,25422663.0,GSM7885888 r2,0:75.53 1:75.43,A:968455256;C:947191550;G:939808490;T:982330983;N:119757,75,75,,,968455256,947191550,939808490,982330983,119757,SRX22410951,SRS19443729,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96615,0.96781,0.0624,0.06196,0.71725,0.71827,0.47042,0.46294,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28822,SRR26711840,SRX22410950,SRS19443727,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  no treatment  replicate 4,GSM7885887,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  no treatment  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant,GSM7885887,GSM7885887: rad21 heterozugous tailbud  no treatment  replicate 4; Danio rerio; RNA Seq,GSM7885887 r1,GSM7885887,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-8-HET_S30_L001_R2_001.fastq.gz Rad21-8-HET_S30_L001_R1_001.fastq.gz,fastq fastq,4150580457.0,27506773.0,GSM7885887 r1,0:75.51 1:75.39,A:1061191322;C:1016515755;G:1039117012;T:1033588629;N:167739,75,75,,,1061191322,1016515755,1039117012,1033588629,167739,SRX22410950,SRS19443727,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96699,0.96687,0.0501,0.04959,0.71642,0.72017,0.44914,0.44833,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28823,SRR26711841,SRX22410950,SRS19443727,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  no treatment  replicate 4,GSM7885887,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  no treatment  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant,GSM7885887,GSM7885887: rad21 heterozugous tailbud  no treatment  replicate 4; Danio rerio; RNA Seq,GSM7885887 r1,GSM7885887,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-8-HET_S30_L002_R2_001.fastq.gz Rad21-8-HET_S30_L002_R1_001.fastq.gz,fastq fastq,4170430033.0,27638560.0,GSM7885887 r2,0:75.50 1:75.39,A:1067297262;C:1021226653;G:1043544460;T:1038184807;N:176851,75,75,,,1067297262,1021226653,1043544460,1038184807,176851,SRX22410950,SRS19443727,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96619,0.96635,0.05062,0.05015,0.7139,0.71918,0.44965,0.45175,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28824,SRR26711842,SRX22410949,SRS19443728,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  no treatment  replicate 4,GSM7885886,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  no treatment  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant,GSM7885886,GSM7885886: rad21 homozygous tailbud  no treatment  replicate 4; Danio rerio; RNA Seq,GSM7885886 r1,GSM7885886,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-4-MUT_S29_L001_R1_001.fastq.gz Rad21-4-MUT_S29_L001_R2_001.fastq.gz,fastq fastq,3860758586.0,25585267.0,GSM7885886 r1,0:75.50 1:75.40,A:962978350;C:961963514;G:957530709;T:978120083;N:165930,75,75,,,962978350,961963514,957530709,978120083,165930,SRX22410949,SRS19443728,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96679,0.96899,0.05708,0.05592,0.71991,0.72021,0.44331,0.44736,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28825,SRR26711843,SRX22410949,SRS19443728,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  no treatment  replicate 4,GSM7885886,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  no treatment  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant,GSM7885886,GSM7885886: rad21 homozygous tailbud  no treatment  replicate 4; Danio rerio; RNA Seq,GSM7885886 r1,GSM7885886,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-4-MUT_S29_L002_R1_001.fastq.gz Rad21-4-MUT_S29_L002_R2_001.fastq.gz,fastq fastq,3886411017.0,25755387.0,GSM7885886 r2,0:75.50 1:75.40,A:969709828;C:968345638;G:963787543;T:984390915;N:177093,75,75,,,969709828,968345638,963787543,984390915,177093,SRX22410949,SRS19443728,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96682,0.96836,0.05697,0.05624,0.71812,0.71819,0.4505,0.44685,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28826,SRR26711844,SRX22410948,SRS19443726,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  Wnt stimulation  replicate 4,GSM7885885,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,stag2b tailbud  Wnt stimulation  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation,GSM7885885,GSM7885885: stag2b tailbud  Wnt stimulation  replicate 4; Danio rerio; RNA Seq,GSM7885885 r1,GSM7885885,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-BIO-4_S28_L001_R1_001.fastq.gz S2B-BIO-4_S28_L001_R2_001.fastq.gz,fastq fastq,3727162917.0,24693169.0,GSM7885885 r1,0:75.53 1:75.41,A:922580573;C:935922329;G:933433047;T:935120514;N:106454,75,75,,,922580573,935922329,933433047,935120514,106454,SRX22410948,SRS19443726,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96731,0.96936,0.04393,0.04403,0.72234,0.72397,0.46015,0.45955,76,74,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28827,SRR26711845,SRX22410948,SRS19443726,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  Wnt stimulation  replicate 4,GSM7885885,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,stag2b tailbud  Wnt stimulation  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation,GSM7885885,GSM7885885: stag2b tailbud  Wnt stimulation  replicate 4; Danio rerio; RNA Seq,GSM7885885 r1,GSM7885885,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-BIO-4_S28_L002_R1_001.fastq.gz S2B-BIO-4_S28_L002_R2_001.fastq.gz,fastq fastq,3749916462.0,24844024.0,GSM7885885 r2,0:75.53 1:75.41,A:928588967;C:941571510;G:939049263;T:940598432;N:108290,75,75,,,928588967,941571510,939049263,940598432,108290,SRX22410948,SRS19443726,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96668,0.96881,0.04401,0.04387,0.72387,0.72519,0.45814,0.457,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28828,SRR26711846,SRX22410947,SRS19443724,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  no treatment  replicate 4,GSM7885884,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing,stag2b tailbud  no treatment  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant,GSM7885884,GSM7885884: stag2b tailbud  no treatment  replicate 4; Danio rerio; RNA Seq,GSM7885884 r1,GSM7885884,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-4_S27_L001_R1_001.fastq.gz S2B-4_S27_L001_R2_001.fastq.gz,fastq fastq,4559287327.0,30217717.0,GSM7885884 r1,0:75.49 1:75.39,A:1129871064;C:1144626195;G:1141080047;T:1143531432;N:178589,75,75,,,1129871064,1144626195,1141080047,1143531432,178589,SRX22410947,SRS19443724,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96507,0.96728,0.04397,0.04385,0.72338,0.72456,0.44876,0.45623,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28829,SRR26711847,SRX22410947,SRS19443724,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  no treatment  replicate 4,GSM7885884,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing,stag2b tailbud  no treatment  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant,GSM7885884,GSM7885884: stag2b tailbud  no treatment  replicate 4; Danio rerio; RNA Seq,GSM7885884 r1,GSM7885884,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-4_S27_L002_R1_001.fastq.gz S2B-4_S27_L002_R2_001.fastq.gz,fastq fastq,4586674313.0,30399355.0,GSM7885884 r2,0:75.49 1:75.39,A:1137101056;C:1151500029;G:1147768493;T:1150129054;N:175681,75,75,,,1137101056,1151500029,1147768493,1150129054,175681,SRX22410947,SRS19443724,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96454,0.96735,0.04449,0.04408,0.72435,0.72583,0.45339,0.45434,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28830,SRR26711848,SRX22410946,SRS19443725,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  Wnt stimulation  replicate 4,GSM7885883,,source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,Wild type tailbud  Wnt stimulation  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation,GSM7885883,GSM7885883: Wild type tailbud  Wnt stimulation  replicate 4; Danio rerio; RNA Seq,GSM7885883 r1,GSM7885883,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT-BIO-4_S26_L001_R2_001.fastq.gz WT-BIO-4_S26_L001_R1_001.fastq.gz,fastq fastq,5251141754.0,34808166.0,GSM7885883 r1,0:75.48 1:75.38,A:1316653671;C:1303617399;G:1296205519;T:1334442750;N:222415,75,75,,,1316653671,1303617399,1296205519,1334442750,222415,SRX22410946,SRS19443725,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96497,0.96673,0.04868,0.04837,0.72332,0.72324,0.47006,0.45832,75,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28831,SRR26711849,SRX22410946,SRS19443725,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  Wnt stimulation  replicate 4,GSM7885883,,source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,Wild type tailbud  Wnt stimulation  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation,GSM7885883,GSM7885883: Wild type tailbud  Wnt stimulation  replicate 4; Danio rerio; RNA Seq,GSM7885883 r1,GSM7885883,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT-BIO-4_S26_L002_R2_001.fastq.gz WT-BIO-4_S26_L002_R1_001.fastq.gz,fastq fastq,5280302307.0,35001391.0,GSM7885883 r2,0:75.48 1:75.38,A:1324401398;C:1310930748;G:1303177704;T:1341576726;N:215731,75,75,,,1324401398,1310930748,1303177704,1341576726,215731,SRX22410946,SRS19443725,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96424,0.96713,0.04917,0.04864,0.72241,0.72271,0.46443,0.45274,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28832,SRR26711850,SRX22410945,SRS19443723,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  no treatment  replicate 4,GSM7885882,,source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing,Wild type tailbud  no treatment  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type,GSM7885882,GSM7885882: Wild type tailbud  no treatment  replicate 4; Danio rerio; RNA Seq,GSM7885882 r1,GSM7885882,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT4_S25_L001_R1_001.fastq.gz WT4_S25_L001_R2_001.fastq.gz,fastq fastq,7405469360.0,49089434.0,GSM7885882 r1,0:75.49 1:75.37,A:1847973647;C:1841169648;G:1840295933;T:1875743550;N:286582,75,75,,,1847973647,1841169648,1840295933,1875743550,286582,SRX22410945,SRS19443723,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96338,0.96738,0.04317,0.04296,0.71737,0.71851,0.45679,0.45543,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28833,SRR26711851,SRX22410945,SRS19443723,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  no treatment  replicate 4,GSM7885882,,source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing,Wild type tailbud  no treatment  replicate 4,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type,GSM7885882,GSM7885882: Wild type tailbud  no treatment  replicate 4; Danio rerio; RNA Seq,GSM7885882 r1,GSM7885882,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT4_S25_L002_R1_001.fastq.gz WT4_S25_L002_R2_001.fastq.gz,fastq fastq,7449020435.0,49378676.0,GSM7885882 r2,0:75.48 1:75.37,A:1859225781;C:1852173354;G:1850890621;T:1886441454;N:289225,75,75,,,1859225781,1852173354,1850890621,1886441454,289225,SRX22410945,SRS19443723,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96307,0.9662,0.04334,0.04269,0.7167,0.71679,0.45909,0.45956,75,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28834,SRR26711852,SRX22410944,SRS19443721,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  Wnt stimulation  replicate 3,GSM7885881,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  Wnt stimulation  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885881,GSM7885881: rad21 heterozugous tailbud  Wnt stimulation  replicate 3; Danio rerio; RNA Seq,GSM7885881 r1,GSM7885881,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-7-HET_S24_L001_R1_001.fastq.gz Rad21-BIO-7-HET_S24_L001_R2_001.fastq.gz,fastq fastq,3984218790.0,26397905.0,GSM7885881 r1,0:75.51 1:75.42,A:1024724878;C:960806363;G:958470013;T:1040115284;N:102252,75,75,,,1024724878,960806363,958470013,1040115284,102252,SRX22410944,SRS19443721,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95932,0.96163,0.06729,0.06702,0.71979,0.71981,0.4528,0.4607,76,74,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28835,SRR26711853,SRX22410944,SRS19443721,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  Wnt stimulation  replicate 3,GSM7885881,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  Wnt stimulation  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885881,GSM7885881: rad21 heterozugous tailbud  Wnt stimulation  replicate 3; Danio rerio; RNA Seq,GSM7885881 r1,GSM7885881,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-7-HET_S24_L002_R1_001.fastq.gz Rad21-BIO-7-HET_S24_L002_R2_001.fastq.gz,fastq fastq,4008829445.0,26560912.0,GSM7885881 r2,0:75.51 1:75.42,A:1031275075;C:966838521;G:964312635;T:1046301501;N:101713,75,75,,,1031275075,966838521,964312635,1046301501,101713,SRX22410944,SRS19443721,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.9587,0.96152,0.06791,0.06665,0.71989,0.72157,0.45962,0.46712,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28836,SRR26711854,SRX22410943,SRS19443722,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  Wnt stimulation  replicate 3,GSM7885880,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  Wnt stimulation  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885880,GSM7885880: rad21 homozygous tailbud  Wnt stimulation  replicate 3; Danio rerio; RNA Seq,GSM7885880 r1,GSM7885880,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-3-MUT_S23_L001_R1_001.fastq.gz Rad21-BIO-3-MUT_S23_L001_R2_001.fastq.gz,fastq fastq,5599192259.0,37097144.0,GSM7885880 r1,0:75.51 1:75.43,A:1432393511;C:1358888032;G:1349825352;T:1457936919;N:148445,75,75,,,1432393511,1358888032,1349825352,1457936919,148445,SRX22410943,SRS19443722,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96008,0.96296,0.0752,0.07458,0.71518,0.71595,0.45869,0.45262,76,74,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28837,SRR26711855,SRX22410943,SRS19443722,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  Wnt stimulation  replicate 3,GSM7885880,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  Wnt stimulation  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885880,GSM7885880: rad21 homozygous tailbud  Wnt stimulation  replicate 3; Danio rerio; RNA Seq,GSM7885880 r1,GSM7885880,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-3-MUT_S23_L002_R1_001.fastq.gz Rad21-BIO-3-MUT_S23_L002_R2_001.fastq.gz,fastq fastq,5635998309.0,37340801.0,GSM7885880 r2,0:75.51 1:75.43,A:1442157325;C:1367898781;G:1358570964;T:1467225614;N:145625,75,75,,,1442157325,1367898781,1358570964,1467225614,145625,SRX22410943,SRS19443722,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95976,0.96205,0.07516,0.07494,0.71415,0.71498,0.4588,0.45974,75,74,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28838,SRR26711856,SRX22410942,SRS19443720,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  no treatment  replicate 3,GSM7885879,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  no treatment  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant,GSM7885879,GSM7885879: rad21 heterozugous tailbud  no treatment  replicate 3; Danio rerio; RNA Seq,GSM7885879 r1,GSM7885879,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-7-HET_S22_L001_R1_001.fastq.gz Rad21-7-HET_S22_L001_R2_001.fastq.gz,fastq fastq,3991372523.0,26445612.0,GSM7885879 r1,0:75.50 1:75.43,A:1041422592;C:951170399;G:942539955;T:1056130915;N:108662,75,75,,,1041422592,951170399,942539955,1056130915,108662,SRX22410942,SRS19443720,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.956,0.9592,0.07986,0.07892,0.71336,0.71407,0.45912,0.45547,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28839,SRR26711857,SRX22410942,SRS19443720,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  no treatment  replicate 3,GSM7885879,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  no treatment  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant,GSM7885879,GSM7885879: rad21 heterozugous tailbud  no treatment  replicate 3; Danio rerio; RNA Seq,GSM7885879 r1,GSM7885879,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-7-HET_S22_L002_R1_001.fastq.gz Rad21-7-HET_S22_L002_R2_001.fastq.gz,fastq fastq,4014736816.0,26600423.0,GSM7885879 r2,0:75.50 1:75.43,A:1047767788;C:956861322;G:947979944;T:1062023242;N:104520,75,75,,,1047767788,956861322,947979944,1062023242,104520,SRX22410942,SRS19443720,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95647,0.9597,0.07844,0.07753,0.71342,0.71449,0.45886,0.45627,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28840,SRR26711858,SRX22410941,SRS19443719,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  no treatment  replicate 3,GSM7885878,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  no treatment  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant,GSM7885878,GSM7885878: rad21 homozygous tailbud  no treatment  replicate 3; Danio rerio; RNA Seq,GSM7885878 r1,GSM7885878,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-3-MUT_S21_L001_R1_001.fastq.gz Rad21-3-MUT_S21_L001_R2_001.fastq.gz,fastq fastq,4087719740.0,27096477.0,GSM7885878 r1,0:75.47 1:75.39,A:1036209125;C:1001425527;G:987804368;T:1062147338;N:133382,75,75,,,1036209125,1001425527,987804368,1062147338,133382,SRX22410941,SRS19443719,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95988,0.9638,0.06968,0.06927,0.71407,0.7136,0.454,0.45623,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28841,SRR26711859,SRX22410941,SRS19443719,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  no treatment  replicate 3,GSM7885878,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  no treatment  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant,GSM7885878,GSM7885878: rad21 homozygous tailbud  no treatment  replicate 3; Danio rerio; RNA Seq,GSM7885878 r1,GSM7885878,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-3-MUT_S21_L002_R1_001.fastq.gz Rad21-3-MUT_S21_L002_R2_001.fastq.gz,fastq fastq,4118276880.0,27299338.0,GSM7885878 r2,0:75.47 1:75.38,A:1044090882;C:1009018215;G:995236418;T:1069786789;N:144576,75,75,,,1044090882,1009018215,995236418,1069786789,144576,SRX22410941,SRS19443719,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96038,0.96408,0.06924,0.06885,0.71405,0.71346,0.46106,0.46176,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28842,SRR26711860,SRX22410940,SRS19443718,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  Wnt stimulation  replicate 3,GSM7885877,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,stag2b tailbud  Wnt stimulation  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation,GSM7885877,GSM7885877: stag2b tailbud  Wnt stimulation  replicate 3; Danio rerio; RNA Seq,GSM7885877 r1,GSM7885877,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-BIO-3_S20_L001_R2_001.fastq.gz S2B-BIO-3_S20_L001_R1_001.fastq.gz,fastq fastq,6393544263.0,42359569.0,GSM7885877 r1,0:75.52 1:75.42,A:1613857834;C:1576676813;G:1555975373;T:1646885701;N:148542,75,75,,,1613857834,1576676813,1555975373,1646885701,148542,SRX22410940,SRS19443718,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96254,0.96412,0.05789,0.05657,0.71928,0.71952,0.45598,0.4571,76,74,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28843,SRR26711861,SRX22410940,SRS19443718,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  Wnt stimulation  replicate 3,GSM7885877,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,stag2b tailbud  Wnt stimulation  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation,GSM7885877,GSM7885877: stag2b tailbud  Wnt stimulation  replicate 3; Danio rerio; RNA Seq,GSM7885877 r1,GSM7885877,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-BIO-3_S20_L002_R1_001.fastq.gz S2B-BIO-3_S20_L002_R2_001.fastq.gz,fastq fastq,6434553541.0,42631351.0,GSM7885877 r2,0:75.52 1:75.42,A:1624553501;C:1586927728;G:1565855680;T:1657071521;N:145111,75,75,,,1624553501,1586927728,1565855680,1657071521,145111,SRX22410940,SRS19443718,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96161,0.96439,0.05708,0.057,0.71877,0.71885,0.45079,0.45162,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28844,SRR26711862,SRX22410939,SRS19443717,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  no treatment  replicate 3,GSM7885876,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing,stag2b tailbud  no treatment  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant,GSM7885876,GSM7885876: stag2b tailbud  no treatment  replicate 3; Danio rerio; RNA Seq,GSM7885876 r1,GSM7885876,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-3_S19_L001_R2_001.fastq.gz S2B-3_S19_L001_R1_001.fastq.gz,fastq fastq,5538483383.0,36711860.0,GSM7885876 r1,0:75.47 1:75.39,A:1435032372;C:1328594066;G:1316913430;T:1457777034;N:166481,75,75,,,1435032372,1328594066,1316913430,1457777034,166481,SRX22410939,SRS19443717,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95388,0.95759,0.06115,0.05971,0.72494,0.72437,0.45251,0.45094,75,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28845,SRR26711863,SRX22410939,SRS19443717,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  no treatment  replicate 3,GSM7885876,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing,stag2b tailbud  no treatment  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant,GSM7885876,GSM7885876: stag2b tailbud  no treatment  replicate 3; Danio rerio; RNA Seq,GSM7885876 r1,GSM7885876,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-3_S19_L002_R2_001.fastq.gz S2B-3_S19_L002_R1_001.fastq.gz,fastq fastq,5571956623.0,36933840.0,GSM7885876 r2,0:75.47 1:75.39,A:1444099757;C:1336600251;G:1324816524;T:1466267099;N:172992,75,75,,,1444099757,1336600251,1324816524,1466267099,172992,SRX22410939,SRS19443717,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95377,0.95715,0.06134,0.06056,0.72342,0.72399,0.45371,0.45229,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28846,SRR26711864,SRX22410938,SRS19443716,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  Wnt stimulation  replicate 3,GSM7885875,,source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,Wild type tailbud  Wnt stimulation  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation,GSM7885875,GSM7885875: Wild type tailbud  Wnt stimulation  replicate 3; Danio rerio; RNA Seq,GSM7885875 r1,GSM7885875,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT-BIO-3_S18_L001_R2_001.fastq.gz WT-BIO-3_S18_L001_R1_001.fastq.gz,fastq fastq,2907588427.0,19272780.0,GSM7885875 r1,0:75.47 1:75.39,A:744742520;C:704673544;G:696135407;T:761933560;N:103396,75,75,,,744742520,704673544,696135407,761933560,103396,SRX22410938,SRS19443716,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95667,0.96068,0.06758,0.06662,0.71654,0.71695,0.46152,0.46391,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28847,SRR26711865,SRX22410938,SRS19443716,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  Wnt stimulation  replicate 3,GSM7885875,,source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,Wild type tailbud  Wnt stimulation  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation,GSM7885875,GSM7885875: Wild type tailbud  Wnt stimulation  replicate 3; Danio rerio; RNA Seq,GSM7885875 r1,GSM7885875,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT-BIO-3_S18_L002_R2_001.fastq.gz WT-BIO-3_S18_L002_R1_001.fastq.gz,fastq fastq,2928304522.0,19409983.0,GSM7885875 r2,0:75.47 1:75.39,A:750212329;C:709699732;G:701107247;T:767185941;N:99273,75,75,,,750212329,709699732,701107247,767185941,99273,SRX22410938,SRS19443716,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95734,0.96043,0.06712,0.06582,0.71764,0.71829,0.46986,0.46257,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28848,SRR26711866,SRX22410937,SRS19443715,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  no treatment  replicate 3,GSM7885874,,source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing,Wild type tailbud  no treatment  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type,GSM7885874,GSM7885874: Wild type tailbud  no treatment  replicate 3; Danio rerio; RNA Seq,GSM7885874 r1,GSM7885874,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT3_S17_L001_R2_001.fastq.gz WT3_S17_L001_R1_001.fastq.gz,fastq fastq,6706792771.0,44471190.0,GSM7885874 r1,0:75.45 1:75.37,A:1721256764;C:1618398945;G:1602221748;T:1764649478;N:265836,75,75,,,1721256764,1618398945,1602221748,1764649478,265836,SRX22410937,SRS19443715,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95476,0.95901,0.0654,0.06441,0.71821,0.71764,0.46826,0.46883,75,73,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28849,SRR26711867,SRX22410937,SRS19443715,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  no treatment  replicate 3,GSM7885874,,source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing,Wild type tailbud  no treatment  replicate 3,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type,GSM7885874,GSM7885874: Wild type tailbud  no treatment  replicate 3; Danio rerio; RNA Seq,GSM7885874 r1,GSM7885874,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT3_S17_L002_R1_001.fastq.gz WT3_S17_L002_R2_001.fastq.gz,fastq fastq,6751557772.0,44768192.0,GSM7885874 r2,0:75.45 1:75.37,A:1732864650;C:1629248349;G:1613082990;T:1776088109;N:273674,75,75,,,1732864650,1629248349,1613082990,1776088109,273674,SRX22410937,SRS19443715,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95584,0.95991,0.0649,0.0638,0.71819,0.71855,0.47015,0.46826,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28850,SRR26711868,SRX22410936,SRS19443714,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  Wnt stimulation  replicate 2,GSM7885873,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  Wnt stimulation  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885873,GSM7885873: rad21 heterozugous tailbud  Wnt stimulation  replicate 2; Danio rerio; RNA Seq,GSM7885873 r1,GSM7885873,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-6-HET_S16_L001_R1_001.fastq.gz Rad21-BIO-6-HET_S16_L001_R2_001.fastq.gz,fastq fastq,10402910048.0,68936909.0,GSM7885873 r1,0:75.49 1:75.41,A:2678222257;C:2507951720;G:2508878864;T:2707580436;N:276771,75,75,,,2678222257,2507951720,2508878864,2707580436,276771,SRX22410936,SRS19443714,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95996,0.96303,0.07074,0.07121,0.7176,0.71977,0.46271,0.46279,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28851,SRR26711869,SRX22410936,SRS19443714,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  Wnt stimulation  replicate 2,GSM7885873,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  Wnt stimulation  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885873,GSM7885873: rad21 heterozugous tailbud  Wnt stimulation  replicate 2; Danio rerio; RNA Seq,GSM7885873 r1,GSM7885873,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-6-HET_S16_L002_R1_001.fastq.gz Rad21-BIO-6-HET_S16_L002_R2_001.fastq.gz,fastq fastq,10457419135.0,69298126.0,GSM7885873 r2,0:75.49 1:75.41,A:2693018275;C:2521215208;G:2521858256;T:2721040335;N:287061,75,75,,,2693018275,2521215208,2521858256,2721040335,287061,SRX22410936,SRS19443714,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95978,0.962,0.07287,0.07218,0.71928,0.72015,0.4627,0.46327,76,74,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28852,SRR26711870,SRX22410935,SRS19443713,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  Wnt stimulation  replicate 2,GSM7885872,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  Wnt stimulation  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885872,GSM7885872: rad21 homozygous tailbud  Wnt stimulation  replicate 2; Danio rerio; RNA Seq,GSM7885872 r1,GSM7885872,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-2-MUT_S15_L001_R2_001.fastq.gz Rad21-BIO-2-MUT_S15_L001_R1_001.fastq.gz,fastq fastq,7186685076.0,47626097.0,GSM7885872 r1,0:75.50 1:75.40,A:1840710532;C:1745543326;G:1746892421;T:1853340863;N:197934,75,75,,,1840710532,1745543326,1746892421,1853340863,197934,SRX22410935,SRS19443713,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96231,0.96418,0.06946,0.06881,0.71756,0.71873,0.46166,0.45998,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28853,SRR26711871,SRX22410935,SRS19443713,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  Wnt stimulation  replicate 2,GSM7885872,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  Wnt stimulation  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885872,GSM7885872: rad21 homozygous tailbud  Wnt stimulation  replicate 2; Danio rerio; RNA Seq,GSM7885872 r1,GSM7885872,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-2-MUT_S15_L002_R2_001.fastq.gz Rad21-BIO-2-MUT_S15_L002_R1_001.fastq.gz,fastq fastq,7224888168.0,47879502.0,GSM7885872 r2,0:75.50 1:75.40,A:1851188490;C:1754962659;G:1755894085;T:1862643357;N:199577,75,75,,,1851188490,1754962659,1755894085,1862643357,199577,SRX22410935,SRS19443713,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96174,0.96335,0.06858,0.06794,0.71624,0.71752,0.46477,0.46238,74,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28854,SRR26711872,SRX22410934,SRS19443712,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  no treatment  replicate 2,GSM7885871,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  no treatment  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant,GSM7885871,GSM7885871: rad21 heterozugous tailbud  no treatment  replicate 2; Danio rerio; RNA Seq,GSM7885871 r1,GSM7885871,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-6-HET_S14_L001_R2_001.fastq.gz Rad21-6-HET_S14_L001_R1_001.fastq.gz,fastq fastq,5920802946.0,39225537.0,GSM7885871 r1,0:75.52 1:75.42,A:1518148809;C:1443498311;G:1449929695;T:1509064332;N:161799,75,75,,,1518148809,1443498311,1449929695,1509064332,161799,SRX22410934,SRS19443712,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96404,0.96544,0.06392,0.06339,0.71825,0.71956,0.45911,0.44993,75,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28855,SRR26711873,SRX22410934,SRS19443712,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  no treatment  replicate 2,GSM7885871,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  no treatment  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant,GSM7885871,GSM7885871: rad21 heterozugous tailbud  no treatment  replicate 2; Danio rerio; RNA Seq,GSM7885871 r1,GSM7885871,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-6-HET_S14_L002_R1_001.fastq.gz Rad21-6-HET_S14_L002_R2_001.fastq.gz,fastq fastq,5948197274.0,39406919.0,GSM7885871 r2,0:75.52 1:75.42,A:1525770407;C:1450296537;G:1456334492;T:1515638367;N:157471,75,75,,,1525770407,1450296537,1456334492,1515638367,157471,SRX22410934,SRS19443712,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.9635,0.96517,0.06272,0.06248,0.71804,0.72202,0.45512,0.45879,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28856,SRR26711874,SRX22410933,SRS19443711,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  no treatment  replicate 2,GSM7885870,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  no treatment  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant,GSM7885870,GSM7885870: rad21 homozygous tailbud  no treatment  replicate 2; Danio rerio; RNA Seq,GSM7885870 r1,GSM7885870,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-9-MUT_S13_L001_R2_001.fastq.gz Rad21-9-MUT_S13_L001_R1_001.fastq.gz,fastq fastq,4731957733.0,31354997.0,GSM7885870 r1,0:75.51 1:75.41,A:1201221275;C:1160116117;G:1163056871;T:1207419408;N:144062,75,75,,,1201221275,1160116117,1163056871,1207419408,144062,SRX22410933,SRS19443711,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96425,0.96472,0.06588,0.06468,0.71687,0.71942,0.4434,0.44236,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28857,SRR26711875,SRX22410933,SRS19443711,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  no treatment  replicate 2,GSM7885870,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  no treatment  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant,GSM7885870,GSM7885870: rad21 homozygous tailbud  no treatment  replicate 2; Danio rerio; RNA Seq,GSM7885870 r1,GSM7885870,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-9-MUT_S13_L002_R1_001.fastq.gz Rad21-9-MUT_S13_L002_R2_001.fastq.gz,fastq fastq,4757933550.0,31527251.0,GSM7885870 r2,0:75.51 1:75.41,A:1208392417;C:1166483269;G:1169184243;T:1213729419;N:144202,75,75,,,1208392417,1166483269,1169184243,1213729419,144202,SRX22410933,SRS19443711,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96375,0.96493,0.06559,0.06422,0.71774,0.71922,0.44693,0.43358,76,74,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28858,SRR26711876,SRX22410932,SRS19443710,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  Wnt stimulation  replicate 2,GSM7885869,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,stag2b tailbud  Wnt stimulation  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation,GSM7885869,GSM7885869: stag2b tailbud  Wnt stimulation  replicate 2; Danio rerio; RNA Seq,GSM7885869 r1,GSM7885869,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-BIO-2_S12_L001_R1_001.fastq.gz S2B-BIO-2_S12_L001_R2_001.fastq.gz,fastq fastq,3434334163.0,22753985.0,GSM7885869 r1,0:75.51 1:75.42,A:874466456;C:839309146;G:839975055;T:880508590;N:74916,75,75,,,874466456,839309146,839975055,880508590,74916,SRX22410932,SRS19443710,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96096,0.96302,0.06063,0.06064,0.71676,0.7177,0.45781,0.45685,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28859,SRR26711877,SRX22410932,SRS19443710,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  Wnt stimulation  replicate 2,GSM7885869,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,stag2b tailbud  Wnt stimulation  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation,GSM7885869,GSM7885869: stag2b tailbud  Wnt stimulation  replicate 2; Danio rerio; RNA Seq,GSM7885869 r1,GSM7885869,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-BIO-2_S12_L002_R1_001.fastq.gz S2B-BIO-2_S12_L002_R2_001.fastq.gz,fastq fastq,3455106879.0,22891438.0,GSM7885869 r2,0:75.52 1:75.42,A:880118959;C:844367467;G:844856793;T:885694827;N:68833,75,75,,,880118959,844367467,844856793,885694827,68833,SRX22410932,SRS19443710,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96044,0.96247,0.06148,0.06124,0.71892,0.72019,0.45384,0.45979,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28860,SRR26711878,SRX22410931,SRS19443708,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  no treatment  replicate 2,GSM7885868,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing,stag2b tailbud  no treatment  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant,GSM7885868,GSM7885868: stag2b tailbud  no treatment  replicate 2; Danio rerio; RNA Seq,GSM7885868 r1,GSM7885868,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-2_S11_L001_R1_001.fastq.gz S2B-2_S11_L001_R2_001.fastq.gz,fastq fastq,3538294337.0,23437308.0,GSM7885868 r1,0:75.53 1:75.44,A:911440182;C:854797688;G:851200714;T:920789817;N:65936,75,75,,,911440182,854797688,851200714,920789817,65936,SRX22410931,SRS19443708,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95621,0.95881,0.06034,0.05969,0.71816,0.71892,0.45142,0.45093,75,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28861,SRR26711879,SRX22410931,SRS19443708,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  no treatment  replicate 2,GSM7885868,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing,stag2b tailbud  no treatment  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant,GSM7885868,GSM7885868: stag2b tailbud  no treatment  replicate 2; Danio rerio; RNA Seq,GSM7885868 r1,GSM7885868,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-2_S11_L002_R1_001.fastq.gz S2B-2_S11_L002_R2_001.fastq.gz,fastq fastq,3556484158.0,23557941.0,GSM7885868 r2,0:75.53 1:75.44,A:916293958;C:859339499;G:855534732;T:925247442;N:68527,75,75,,,916293958,859339499,855534732,925247442,68527,SRX22410931,SRS19443708,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95449,0.95714,0.05993,0.05895,0.7207,0.72174,0.44213,0.44014,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28862,SRR26711880,SRX22410930,SRS19443709,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  Wnt stimulation  replicate 2,GSM7885867,,source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,Wild type tailbud  Wnt stimulation  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation,GSM7885867,GSM7885867: Wild type tailbud  Wnt stimulation  replicate 2; Danio rerio; RNA Seq,GSM7885867 r1,GSM7885867,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT-BIO-2_S10_L001_R1_001.fastq.gz WT-BIO-2_S10_L001_R2_001.fastq.gz,fastq fastq,4962467069.0,32885292.0,GSM7885867 r1,0:75.49 1:75.41,A:1261895016;C:1212881283;G:1199367390;T:1288195310;N:128070,75,75,,,1261895016,1212881283,1199367390,1288195310,128070,SRX22410930,SRS19443709,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96086,0.96361,0.06058,0.05969,0.71679,0.71614,0.46741,0.47167,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28863,SRR26711881,SRX22410930,SRS19443709,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  Wnt stimulation  replicate 2,GSM7885867,,source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,Wild type tailbud  Wnt stimulation  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation,GSM7885867,GSM7885867: Wild type tailbud  Wnt stimulation  replicate 2; Danio rerio; RNA Seq,GSM7885867 r1,GSM7885867,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT-BIO-2_S10_L002_R1_001.fastq.gz WT-BIO-2_S10_L002_R2_001.fastq.gz,fastq fastq,4987807658.0,33053054.0,GSM7885867 r2,0:75.50 1:75.41,A:1268585681;C:1219140011;G:1205507373;T:1294443086;N:131507,75,75,,,1268585681,1219140011,1205507373,1294443086,131507,SRX22410930,SRS19443709,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96019,0.96278,0.0598,0.05932,0.71837,0.71942,0.46581,0.46052,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28864,SRR26711882,SRX22410929,SRS19443707,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  no treatment  replicate 2,GSM7885866,,source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing,Wild type tailbud  no treatment  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type,GSM7885866,GSM7885866: Wild type tailbud  no treatment  replicate 2; Danio rerio; RNA Seq,GSM7885866 r1,GSM7885866,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT2_S9_L001_R1_001.fastq.gz WT2_S9_L001_R2_001.fastq.gz,fastq fastq,4886840867.0,32385548.0,GSM7885866 r1,0:75.49 1:75.41,A:1236862700;C:1194914216;G:1187547323;T:1267379660;N:136968,75,75,,,1236862700,1194914216,1187547323,1267379660,136968,SRX22410929,SRS19443707,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95919,0.96199,0.05896,0.0586,0.71555,0.71587,0.46036,0.46125,76,74,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28865,SRR26711883,SRX22410929,SRS19443707,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  no treatment  replicate 2,GSM7885866,,source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing,Wild type tailbud  no treatment  replicate 2,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type,GSM7885866,GSM7885866: Wild type tailbud  no treatment  replicate 2; Danio rerio; RNA Seq,GSM7885866 r1,GSM7885866,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT2_S9_L002_R1_001.fastq.gz WT2_S9_L002_R2_001.fastq.gz,fastq fastq,4916008107.0,32579134.0,GSM7885866 r2,0:75.49 1:75.40,A:1244399521;C:1202192346;G:1194561433;T:1274714960;N:139847,75,75,,,1244399521,1202192346,1194561433,1274714960,139847,SRX22410929,SRS19443707,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.95906,0.9626,0.05798,0.05754,0.71502,0.71526,0.46094,0.45988,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28866,SRR26711884,SRX22410928,SRS19443706,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  Wnt stimulation  replicate 1,GSM7885865,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  Wnt stimulation  replicate 1,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885865,GSM7885865: rad21 heterozugous tailbud  Wnt stimulation  replicate 1; Danio rerio; RNA Seq,GSM7885865 r1,GSM7885865,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-5-HET_S8_L001_R1_001.fastq.gz Rad21-BIO-5-HET_S8_L001_R2_001.fastq.gz,fastq fastq,3066593621.0,20312935.0,GSM7885865 r1,0:75.54 1:75.43,A:773539057;C:758309818;G:762855989;T:771829322;N:59435,75,75,,,773539057,758309818,762855989,771829322,59435,SRX22410928,SRS19443706,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.93814,0.93898,0.05206,0.05092,0.72403,0.72606,0.45323,0.45594,76,74,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28867,SRR26711885,SRX22410928,SRS19443706,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  Wnt stimulation  replicate 1,GSM7885865,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  Wnt stimulation  replicate 1,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885865,GSM7885865: rad21 heterozugous tailbud  Wnt stimulation  replicate 1; Danio rerio; RNA Seq,GSM7885865 r1,GSM7885865,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-5-HET_S8_L002_R1_001.fastq.gz Rad21-BIO-5-HET_S8_L002_R2_001.fastq.gz,fastq fastq,3080824265.0,20407318.0,GSM7885865 r2,0:75.54 1:75.43,A:777565943;C:761729558;G:766237246;T:775229684;N:61834,75,75,,,777565943,761729558,766237246,775229684,61834,SRX22410928,SRS19443706,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.93811,0.93851,0.0524,0.05135,0.72403,0.72689,0.45207,0.46155,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28868,SRR26711886,SRX22410927,SRS19443704,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  Wnt stimulation  replicate 1,GSM7885864,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  Wnt stimulation  replicate 1,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885864,GSM7885864: rad21 homozygous tailbud  Wnt stimulation  replicate 1; Danio rerio; RNA Seq,GSM7885864 r1,GSM7885864,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-1-MUT_S7_L001_R1_001.fastq.gz Rad21-BIO-1-MUT_S7_L001_R2_001.fastq.gz,fastq fastq,4788638898.0,31734845.0,GSM7885864 r1,0:75.51 1:75.38,A:1180996230;C:1208056992;G:1207225278;T:1192209164;N:151234,75,75,,,1180996230,1208056992,1207225278,1192209164,151234,SRX22410927,SRS19443704,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.971,0.97197,0.04922,0.04884,0.72342,0.72571,0.46723,0.46582,75,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28869,SRR26711887,SRX22410927,SRS19443704,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  Wnt stimulation  replicate 1,GSM7885864,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  Wnt stimulation  replicate 1,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation,GSM7885864,GSM7885864: rad21 homozygous tailbud  Wnt stimulation  replicate 1; Danio rerio; RNA Seq,GSM7885864 r1,GSM7885864,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-BIO-1-MUT_S7_L002_R1_001.fastq.gz Rad21-BIO-1-MUT_S7_L002_R2_001.fastq.gz,fastq fastq,4815323290.0,31911994.0,GSM7885864 r2,0:75.51 1:75.38,A:1187948393;C:1214824723;G:1213764297;T:1198630801;N:155076,75,75,,,1187948393,1214824723,1213764297,1198630801,155076,SRX22410927,SRS19443704,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.97042,0.97163,0.04919,0.04822,0.72575,0.72725,0.46784,0.46687,75,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28870,SRR26711888,SRX22410926,SRS19443705,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  no treatment  replicate 1,GSM7885863,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  no treatment  replicate 1,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant,GSM7885863,GSM7885863: rad21 heterozugous tailbud  no treatment  replicate 1; Danio rerio; RNA Seq,GSM7885863 r1,GSM7885863,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-5-HET_S6_L001_R1_001.fastq.gz Rad21-5-HET_S6_L001_R2_001.fastq.gz,fastq fastq,4731947877.0,31344805.0,GSM7885863 r1,0:75.54 1:75.42,A:1174667885;C:1187877616;G:1186233757;T:1183073645;N:94974,75,75,,,1174667885,1187877616,1186233757,1183073645,94974,SRX22410926,SRS19443705,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.97019,0.97104,0.04787,0.04709,0.72013,0.72157,0.45904,0.4534,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28871,SRR26711889,SRX22410926,SRS19443705,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 heterozugous tailbud  no treatment  replicate 1,GSM7885863,,source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 heterozugous tailbud  no treatment  replicate 1,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:heterozygous rad21 mutant,GSM7885863,GSM7885863: rad21 heterozugous tailbud  no treatment  replicate 1; Danio rerio; RNA Seq,GSM7885863 r1,GSM7885863,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-5-HET_S6_L002_R2_001.fastq.gz Rad21-5-HET_S6_L002_R1_001.fastq.gz,fastq fastq,4753935677.0,31490466.0,GSM7885863 r2,0:75.54 1:75.42,A:1180603224;C:1193421384;G:1191530186;T:1188281161;N:99722,75,75,,,1180603224,1193421384,1191530186,1188281161,99722,SRX22410926,SRS19443705,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96921,0.97138,0.04824,0.04771,0.72135,0.72253,0.4575,0.45266,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28872,SRR26711890,SRX22410925,SRS19443703,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  no treatment  replicate 1,GSM7885862,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  no treatment  replicate 1,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant,GSM7885862,GSM7885862: rad21 homozygous tailbud  no treatment  replicate 1; Danio rerio; RNA Seq,GSM7885862 r1,GSM7885862,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-1-MUT_S5_L001_R1_001.fastq.gz Rad21-1-MUT_S5_L001_R2_001.fastq.gz,fastq fastq,4118085890.0,27306618.0,GSM7885862 r1,0:75.47 1:75.34,A:1025300027;C:1029335773;G:1030828275;T:1032469485;N:152330,75,75,,,1025300027,1029335773,1030828275,1032469485,152330,SRX22410925,SRS19443703,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96791,0.96862,0.05188,0.0515,0.72013,0.72015,0.4522,0.4471,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28873,SRR26711891,SRX22410925,SRS19443703,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,rad21 homozygous tailbud  no treatment  replicate 1,GSM7885862,,source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing,rad21 homozygous tailbud  no treatment  replicate 1,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous rad21 mutant,GSM7885862,GSM7885862: rad21 homozygous tailbud  no treatment  replicate 1; Danio rerio; RNA Seq,GSM7885862 r1,GSM7885862,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,Rad21-1-MUT_S5_L002_R1_001.fastq.gz Rad21-1-MUT_S5_L002_R2_001.fastq.gz,fastq fastq,4146986760.0,27498264.0,GSM7885862 r2,0:75.47 1:75.34,A:1032908199;C:1036610487;G:1037792727;T:1039516300;N:159047,75,75,,,1032908199,1036610487,1037792727,1039516300,159047,SRX22410925,SRS19443703,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96742,0.96892,0.05165,0.05113,0.71918,0.72068,0.45142,0.45319,76,74,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28874,SRR26711892,SRX22410924,SRS19443702,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  Wnt stimulation  replicate 1,GSM7885861,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,stag2b tailbud  Wnt stimulation  replicate 1,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation,GSM7885861,GSM7885861: stag2b tailbud  Wnt stimulation  replicate 1; Danio rerio; RNA Seq,GSM7885861 r1,GSM7885861,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-BIO-1_S4_L001_R2_001.fastq.gz S2B-BIO-1_S4_L001_R1_001.fastq.gz,fastq fastq,2897013924.0,19254896.0,GSM7885861 r1,0:75.29 1:75.17,A:741141530;C:706870086;G:710814654;T:738037384;N:150270,75,75,,,741141530,706870086,710814654,738037384,150270,SRX22410924,SRS19443702,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96485,0.96632,0.05089,0.05075,0.72423,0.72638,0.46419,0.4639,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28875,SRR26711893,SRX22410924,SRS19443702,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  Wnt stimulation  replicate 1,GSM7885861,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,stag2b tailbud  Wnt stimulation  replicate 1,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation,GSM7885861,GSM7885861: stag2b tailbud  Wnt stimulation  replicate 1; Danio rerio; RNA Seq,GSM7885861 r1,GSM7885861,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-BIO-1_S4_L002_R1_001.fastq.gz S2B-BIO-1_S4_L002_R2_001.fastq.gz,fastq fastq,2915617733.0,19378751.0,GSM7885861 r2,0:75.29 1:75.17,A:746370200;C:711440488;G:715102603;T:742552430;N:152012,75,75,,,746370200,711440488,715102603,742552430,152012,SRX22410924,SRS19443702,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96529,0.96741,0.05064,0.05044,0.72397,0.7259,0.47066,0.47479,75,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28876,SRR26711894,SRX22410923,SRS19443701,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  no treatment  replicate 1,GSM7885860,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing,stag2b tailbud  no treatment  replicate 1,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant,GSM7885860,GSM7885860: stag2b tailbud  no treatment  replicate 1; Danio rerio; RNA Seq,GSM7885860 r1,GSM7885860,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-1_S3_L001_R1_001.fastq.gz S2B-1_S3_L001_R2_001.fastq.gz,fastq fastq,4816347042.0,31912880.0,GSM7885860 r1,0:75.52 1:75.40,A:1186516295;C:1215887273;G:1212449212;T:1201357694;N:136568,75,75,,,1186516295,1215887273,1212449212,1201357694,136568,SRX22410923,SRS19443701,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96723,0.96949,0.03922,0.039,0.72417,0.72563,0.44797,0.44612,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28877,SRR26711895,SRX22410923,SRS19443701,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,stag2b tailbud  no treatment  replicate 1,GSM7885860,,source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing,stag2b tailbud  no treatment  replicate 1,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:homozygous stag2b mutant,GSM7885860,GSM7885860: stag2b tailbud  no treatment  replicate 1; Danio rerio; RNA Seq,GSM7885860 r1,GSM7885860,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,S2B-1_S3_L002_R1_001.fastq.gz S2B-1_S3_L002_R2_001.fastq.gz,fastq fastq,4844499098.0,32099402.0,GSM7885860 r2,0:75.52 1:75.40,A:1193956975;C:1222998516;G:1219273844;T:1208134191;N:135572,75,75,,,1193956975,1222998516,1219273844,1208134191,135572,SRX22410923,SRS19443701,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.9673,0.96927,0.03901,0.03847,0.72265,0.7237,0.44466,0.44733,75,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28878,SRR26711896,SRX22410922,SRS19443700,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  Wnt stimulation  replicate 1,GSM7885859,,source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,Wild type tailbud  Wnt stimulation  replicate 1,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation,GSM7885859,GSM7885859: Wild type tailbud  Wnt stimulation  replicate 1; Danio rerio; RNA Seq,GSM7885859 r1,GSM7885859,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT-BIO-1_S2_L001_R1_001.fastq.gz WT-BIO-1_S2_L001_R2_001.fastq.gz,fastq fastq,5412178875.0,35866424.0,GSM7885859 r1,0:75.51 1:75.39,A:1366497169;C:1337079143;G:1340668569;T:1367824895;N:109099,75,75,,,1366497169,1337079143,1340668569,1367824895,109099,SRX22410922,SRS19443700,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96469,0.96636,0.05031,0.04926,0.71792,0.71985,0.46735,0.46003,76,76,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28879,SRR26711897,SRX22410922,SRS19443700,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  Wnt stimulation  replicate 1,GSM7885859,,source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing,Wild type tailbud  Wnt stimulation  replicate 1,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation,GSM7885859,GSM7885859: Wild type tailbud  Wnt stimulation  replicate 1; Danio rerio; RNA Seq,GSM7885859 r1,GSM7885859,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT-BIO-1_S2_L002_R1_001.fastq.gz WT-BIO-1_S2_L002_R2_001.fastq.gz,fastq fastq,5439582943.0,36048596.0,GSM7885859 r2,0:75.50 1:75.39,A:1374188816;C:1343757292;G:1347041961;T:1374478321;N:116553,75,75,,,1374188816,1343757292,1347041961,1374478321,116553,SRX22410922,SRS19443700,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96388,0.96569,0.04966,0.04871,0.71959,0.72141,0.46438,0.47241,76,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28880,SRR26711898,SRX22410921,SRS19443699,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  no treatment  replicate 1,GSM7885858,,source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing,Wild type tailbud  no treatment  replicate 1,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type,GSM7885858,GSM7885858: Wild type tailbud  no treatment  replicate 1; Danio rerio; RNA Seq,GSM7885858 r1,GSM7885858,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT1_S1_L001_R2_001.fastq.gz WT1_S1_L001_R1_001.fastq.gz,fastq fastq,4648127675.0,30828112.0,GSM7885858 r1,0:75.45 1:75.32,A:1143762350;C:1169301499;G:1170916895;T:1163919823;N:227108,75,75,,,1143762350,1169301499,1170916895,1163919823,227108,SRX22410921,SRS19443699,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96756,0.96895,0.03865,0.03806,0.73275,0.73521,0.4512,0.44878,74,74,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
28881,SRR26711899,SRX22410921,SRS19443699,SRP470622,PRJNA1036688,Cohesin composition and dosage independently affect early development in zebrafish,GSE247246,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos  as well as those with homozygous and heterozygous rad21 mutations  and homozygous stag2b mutations. The dataset includes both  baseline samples as well as  samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.,,pubmed:38975838,,Wild type tailbud  no treatment  replicate 1,GSM7885858,,source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing,Wild type tailbud  no treatment  replicate 1,Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups,tailbud,2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,E3 media 28 C,tissue:tailbud|genotype:wild type,GSM7885858,GSM7885858: Wild type tailbud  no treatment  replicate 1; Danio rerio; RNA Seq,GSM7885858 r1,GSM7885858,1,RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen  Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina  USA and TruSeq RNA CD Index Plate Illumina  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP470622,,loader:fastq load.py,WT1_S1_L002_R1_001.fastq.gz WT1_S1_L002_R2_001.fastq.gz,fastq fastq,4676143483.0,31014103.0,GSM7885858 r2,0:75.45 1:75.32,A:1151068941;C:1176347620;G:1177720113;T:1170778976;N:227833,75,75,,,1151068941,1176347620,1177720113,1170778976,227833,SRX22410921,SRS19443699,SRA1747076,"Chromosome Structure and Development, Pathology, Otago University","Chromosome Structure and Development, Pathology, Otago University",2,0.96645,0.96872,0.03855,0.03822,0.73486,0.73513,0.4505,0.4476,73,75,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,sc_generic,single_cell_generic,generic-scrnaseq-only,,New Zealand,2023-11-07,Multi-stage,Embryo,Tail,Multi-system
29031,SRR26989303,SRX22682429,SRS19676381,SRP474934,PRJNA1046494,Cohesin composition and dosage independently affect early development in zebrafish,GSE248952,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,pubmed:38975838,,TB  dissected  stag2b NZ207  scRNA seq,GSM7923481,,source name:tailbud|tissue:tailbud|age:16 hpf|genotype:stag2b NZ207|geo loc name:missing|collection date:missing,TB  dissected  stag2b NZ207  scRNA seq,FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files,tailbud,,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,tissue:tailbud|age:16 hpf|genotype:stag2b NZ207,GSM7923481,GSM7923481: TB  dissected  stag2b NZ207  scRNA seq; Danio rerio; RNA Seq,GSM7923481 r1,GSM7923481,1,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP474934,,loader:fastq load.py,S2B_bamtofastq_S1_L003_I1_001.fastq.gz S2B_bamtofastq_S1_L003_R1_001.fastq.gz S2B_bamtofastq_S1_L003_R2_001.fastq.gz,fastq fastq fastq,31750000000.0,250000000.0,GSM7923481 r1,0:8 1:28 2:91,A:6537438301;C:4417903496;G:5047922141;T:6745922724;N:813338,8,28,91,,6537438301,4417903496,5047922141,6745922724,813338,SRX22682429,SRS19676381,SRA1760034,"Chromosome structure and development group, Pathology, University of Otago","Chromosome structure and development group, Pathology, University of Otago",1,0.93608,,0.14792,,0.92462,,0.51672,,91,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,New Zealand,2023-11-29,Segmentation,Embryo,Tail,Multi-system
29032,SRR26989304,SRX22682429,SRS19676381,SRP474934,PRJNA1046494,Cohesin composition and dosage independently affect early development in zebrafish,GSE248952,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,pubmed:38975838,,TB  dissected  stag2b NZ207  scRNA seq,GSM7923481,,source name:tailbud|tissue:tailbud|age:16 hpf|genotype:stag2b NZ207|geo loc name:missing|collection date:missing,TB  dissected  stag2b NZ207  scRNA seq,FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files,tailbud,,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,tissue:tailbud|age:16 hpf|genotype:stag2b NZ207,GSM7923481,GSM7923481: TB  dissected  stag2b NZ207  scRNA seq; Danio rerio; RNA Seq,GSM7923481 r1,GSM7923481,1,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP474934,,loader:fastq load.py,S2B_bamtofastq_S1_L003_I1_002.fastq.gz S2B_bamtofastq_S1_L003_R1_002.fastq.gz S2B_bamtofastq_S1_L003_R2_002.fastq.gz,fastq fastq fastq,31750000000.0,250000000.0,GSM7923481 r2,0:8 1:28 2:91,A:6518388158;C:4725153194;G:5205254633;T:6300375689;N:828326,8,28,91,,6518388158,4725153194,5205254633,6300375689,828326,SRX22682429,SRS19676381,SRA1760034,"Chromosome structure and development group, Pathology, University of Otago","Chromosome structure and development group, Pathology, University of Otago",1,0.95154,,0.12683,,0.92429,,0.45021,,91,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,New Zealand,2023-11-29,Segmentation,Embryo,Tail,Multi-system
29033,SRR26989305,SRX22682429,SRS19676381,SRP474934,PRJNA1046494,Cohesin composition and dosage independently affect early development in zebrafish,GSE248952,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,pubmed:38975838,,TB  dissected  stag2b NZ207  scRNA seq,GSM7923481,,source name:tailbud|tissue:tailbud|age:16 hpf|genotype:stag2b NZ207|geo loc name:missing|collection date:missing,TB  dissected  stag2b NZ207  scRNA seq,FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files,tailbud,,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,tissue:tailbud|age:16 hpf|genotype:stag2b NZ207,GSM7923481,GSM7923481: TB  dissected  stag2b NZ207  scRNA seq; Danio rerio; RNA Seq,GSM7923481 r1,GSM7923481,1,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP474934,,loader:fastq load.py,S2B_bamtofastq_S1_L003_I1_003.fastq.gz S2B_bamtofastq_S1_L003_R1_003.fastq.gz S2B_bamtofastq_S1_L003_R2_003.fastq.gz,fastq fastq fastq,31750000000.0,250000000.0,GSM7923481 r3,0:8 1:28 2:91,A:6383119961;C:4804063495;G:5444337911;T:6117664552;N:814081,8,28,91,,6383119961,4804063495,5444337911,6117664552,814081,SRX22682429,SRS19676381,SRA1760034,"Chromosome structure and development group, Pathology, University of Otago","Chromosome structure and development group, Pathology, University of Otago",1,0.94222,,0.11028,,0.93052,,0.61281,,91,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,New Zealand,2023-11-29,Segmentation,Embryo,Tail,Multi-system
29034,SRR26989306,SRX22682429,SRS19676381,SRP474934,PRJNA1046494,Cohesin composition and dosage independently affect early development in zebrafish,GSE248952,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,pubmed:38975838,,TB  dissected  stag2b NZ207  scRNA seq,GSM7923481,,source name:tailbud|tissue:tailbud|age:16 hpf|genotype:stag2b NZ207|geo loc name:missing|collection date:missing,TB  dissected  stag2b NZ207  scRNA seq,FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files,tailbud,,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,tissue:tailbud|age:16 hpf|genotype:stag2b NZ207,GSM7923481,GSM7923481: TB  dissected  stag2b NZ207  scRNA seq; Danio rerio; RNA Seq,GSM7923481 r1,GSM7923481,1,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP474934,,loader:fastq load.py,S2B_bamtofastq_S1_L003_I1_004.fastq.gz S2B_bamtofastq_S1_L003_R1_004.fastq.gz S2B_bamtofastq_S1_L003_R2_004.fastq.gz,fastq fastq fastq,31750000000.0,250000000.0,GSM7923481 r4,0:8 1:28 2:91,A:6402125828;C:4842822163;G:5314139669;T:6190088524;N:823816,8,28,91,,6402125828,4842822163,5314139669,6190088524,823816,SRX22682429,SRS19676381,SRA1760034,"Chromosome structure and development group, Pathology, University of Otago","Chromosome structure and development group, Pathology, University of Otago",1,0.94588,,0.13163,,0.91747,,0.45552,,91,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,New Zealand,2023-11-29,Segmentation,Embryo,Tail,Multi-system
29035,SRR26989307,SRX22682429,SRS19676381,SRP474934,PRJNA1046494,Cohesin composition and dosage independently affect early development in zebrafish,GSE248952,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,pubmed:38975838,,TB  dissected  stag2b NZ207  scRNA seq,GSM7923481,,source name:tailbud|tissue:tailbud|age:16 hpf|genotype:stag2b NZ207|geo loc name:missing|collection date:missing,TB  dissected  stag2b NZ207  scRNA seq,FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files,tailbud,,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,tissue:tailbud|age:16 hpf|genotype:stag2b NZ207,GSM7923481,GSM7923481: TB  dissected  stag2b NZ207  scRNA seq; Danio rerio; RNA Seq,GSM7923481 r1,GSM7923481,1,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP474934,,loader:fastq load.py,S2B_bamtofastq_S1_L003_I1_005.fastq.gz S2B_bamtofastq_S1_L003_R1_005.fastq.gz S2B_bamtofastq_S1_L003_R2_005.fastq.gz,fastq fastq fastq,21091269095.0,166072985.0,GSM7923481 r5,0:8 1:28 2:91,A:4762107201;C:2885106776;G:3288050363;T:4175805779;N:1571516,8,28,91,,4762107201,2885106776,3288050363,4175805779,1571516,SRX22682429,SRS19676381,SRA1760034,"Chromosome structure and development group, Pathology, University of Otago","Chromosome structure and development group, Pathology, University of Otago",1,0.85155,,0.18636,,0.94314,,0.62392,,91,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,New Zealand,2023-11-29,Segmentation,Embryo,Tail,Multi-system
29036,SRR26989308,SRX22682428,SRS19676380,SRP474934,PRJNA1046494,Cohesin composition and dosage independently affect early development in zebrafish,GSE248952,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,pubmed:38975838,,TB  dissected  wild type  scRNA seq,GSM7923480,,source name:tailbud|tissue:tailbud|age:16 hpf|genotype:AB wild type|geo loc name:missing|collection date:missing,TB  dissected  wild type  scRNA seq,FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files,tailbud,,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,tissue:tailbud|age:16 hpf|genotype:AB wild type,GSM7923480,GSM7923480: TB  dissected  wild type  scRNA seq; Danio rerio; RNA Seq,GSM7923480 r1,GSM7923480,1,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP474934,,loader:fastq load.py,WT_bamtofastq_S1_L003_I1_001.fastq.gz WT_bamtofastq_S1_L003_R1_001.fastq.gz WT_bamtofastq_S1_L003_R2_001.fastq.gz,fastq fastq fastq,31750000000.0,250000000.0,GSM7923480 r1,0:8 1:28 2:91,A:6487643595;C:4511110883;G:5076824945;T:6673593696;N:826881,8,28,91,,6487643595,4511110883,5076824945,6673593696,826881,SRX22682428,SRS19676380,SRA1760034,"Chromosome structure and development group, Pathology, University of Otago","Chromosome structure and development group, Pathology, University of Otago",1,0.95134,,0.14233,,0.91816,,0.48251,,91,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,New Zealand,2023-11-29,Segmentation,Embryo,Tail,Multi-system
29037,SRR26989309,SRX22682428,SRS19676380,SRP474934,PRJNA1046494,Cohesin composition and dosage independently affect early development in zebrafish,GSE248952,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,pubmed:38975838,,TB  dissected  wild type  scRNA seq,GSM7923480,,source name:tailbud|tissue:tailbud|age:16 hpf|genotype:AB wild type|geo loc name:missing|collection date:missing,TB  dissected  wild type  scRNA seq,FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files,tailbud,,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,tissue:tailbud|age:16 hpf|genotype:AB wild type,GSM7923480,GSM7923480: TB  dissected  wild type  scRNA seq; Danio rerio; RNA Seq,GSM7923480 r1,GSM7923480,1,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP474934,,loader:fastq load.py,WT_bamtofastq_S1_L003_I1_002.fastq.gz WT_bamtofastq_S1_L003_R1_002.fastq.gz WT_bamtofastq_S1_L003_R2_002.fastq.gz,fastq fastq fastq,31750000000.0,250000000.0,GSM7923480 r2,0:8 1:28 2:91,A:6572631256;C:4794881740;G:5255235646;T:6126414633;N:836725,8,28,91,,6572631256,4794881740,5255235646,6126414633,836725,SRX22682428,SRS19676380,SRA1760034,"Chromosome structure and development group, Pathology, University of Otago","Chromosome structure and development group, Pathology, University of Otago",1,0.96222,,0.11199,,0.92332,,0.50319,,91,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,New Zealand,2023-11-29,Segmentation,Embryo,Tail,Multi-system
29038,SRR26989310,SRX22682428,SRS19676380,SRP474934,PRJNA1046494,Cohesin composition and dosage independently affect early development in zebrafish,GSE248952,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,pubmed:38975838,,TB  dissected  wild type  scRNA seq,GSM7923480,,source name:tailbud|tissue:tailbud|age:16 hpf|genotype:AB wild type|geo loc name:missing|collection date:missing,TB  dissected  wild type  scRNA seq,FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files,tailbud,,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,tissue:tailbud|age:16 hpf|genotype:AB wild type,GSM7923480,GSM7923480: TB  dissected  wild type  scRNA seq; Danio rerio; RNA Seq,GSM7923480 r1,GSM7923480,1,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP474934,,loader:fastq load.py,WT_bamtofastq_S1_L003_I1_003.fastq.gz WT_bamtofastq_S1_L003_R1_003.fastq.gz WT_bamtofastq_S1_L003_R2_003.fastq.gz,fastq fastq fastq,31750000000.0,250000000.0,GSM7923480 r3,0:8 1:28 2:91,A:6367741226;C:4801321001;G:5377991533;T:6202112567;N:833673,8,28,91,,6367741226,4801321001,5377991533,6202112567,833673,SRX22682428,SRS19676380,SRA1760034,"Chromosome structure and development group, Pathology, University of Otago","Chromosome structure and development group, Pathology, University of Otago",1,0.95193,,0.10884,,0.91362,,0.55405,,91,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,New Zealand,2023-11-29,Segmentation,Embryo,Tail,Multi-system
29039,SRR26989311,SRX22682428,SRS19676380,SRP474934,PRJNA1046494,Cohesin composition and dosage independently affect early development in zebrafish,GSE248952,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,pubmed:38975838,,TB  dissected  wild type  scRNA seq,GSM7923480,,source name:tailbud|tissue:tailbud|age:16 hpf|genotype:AB wild type|geo loc name:missing|collection date:missing,TB  dissected  wild type  scRNA seq,FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files,tailbud,,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,tissue:tailbud|age:16 hpf|genotype:AB wild type,GSM7923480,GSM7923480: TB  dissected  wild type  scRNA seq; Danio rerio; RNA Seq,GSM7923480 r1,GSM7923480,1,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP474934,,loader:fastq load.py,WT_bamtofastq_S1_L003_I1_004.fastq.gz WT_bamtofastq_S1_L003_R1_004.fastq.gz WT_bamtofastq_S1_L003_R2_004.fastq.gz,fastq fastq fastq,31750000000.0,250000000.0,GSM7923480 r4,0:8 1:28 2:91,A:6643013514;C:4783035829;G:5148972841;T:6173682231;N:1295585,8,28,91,,6643013514,4783035829,5148972841,6173682231,1295585,SRX22682428,SRS19676380,SRA1760034,"Chromosome structure and development group, Pathology, University of Otago","Chromosome structure and development group, Pathology, University of Otago",1,0.9356,,0.12122,,0.92084,,0.52901,,91,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,New Zealand,2023-11-29,Segmentation,Embryo,Tail,Multi-system
29040,SRR26989312,SRX22682428,SRS19676380,SRP474934,PRJNA1046494,Cohesin composition and dosage independently affect early development in zebrafish,GSE248952,Transcriptome Analysis,Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,pubmed:38975838,,TB  dissected  wild type  scRNA seq,GSM7923480,,source name:tailbud|tissue:tailbud|age:16 hpf|genotype:AB wild type|geo loc name:missing|collection date:missing,TB  dissected  wild type  scRNA seq,FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files,tailbud,,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,tissue:tailbud|age:16 hpf|genotype:AB wild type,GSM7923480,GSM7923480: TB  dissected  wild type  scRNA seq; Danio rerio; RNA Seq,GSM7923480 r1,GSM7923480,1,Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP474934,,loader:fastq load.py,WT_bamtofastq_S1_L003_I1_005.fastq.gz WT_bamtofastq_S1_L003_R1_005.fastq.gz WT_bamtofastq_S1_L003_R2_005.fastq.gz,fastq fastq fastq,3129498186.0,24641718.0,GSM7923480 r5,0:8 1:28 2:91,A:797078402;C:362323092;G:517613944;T:564921437;N:459463,8,28,91,,797078402,362323092,517613944,564921437,459463,SRX22682428,SRS19676380,SRA1760034,"Chromosome structure and development group, Pathology, University of Otago","Chromosome structure and development group, Pathology, University of Otago",1,0.65184,,0.40446,,0.95262,,0.62704,,91,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,New Zealand,2023-11-29,Segmentation,Embryo,Tail,Multi-system
32781,SRR29411985,SRX24925451,SRS21630866,SRP513930,PRJNA1124008,Cell state transitions are decoupled from cell division during early embryo development [II],GSE269848,Other,Paper abstract: As tissues develop  cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation  we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. However  in the absence of cell division  differentiation slows down in some cell types  and cells exhibit global stress responses. While differentiation is robust to blocking cell division  the proportions of cells across cell states are not but show evidence of partial compensation. This work clarifies our understanding of the role of cell division in development and showcases the utility of combining embryo wide perturbations with single cell RNA sequencing to uncover the role of common biological processes across multiple tissues. Overall design: Design of experiment for this particular dataset: Forty tails from zebrafish embryos at 24  38 hpf and 48 hpf were collected. Cells were dissociated from these tails and multi seq tags were added to the cells for each time point. Cells from all time points were pooled and single cell sequencing was performed using Indrops. Four gene expression GEX libraries were prepared for transcriptomic information and four multiseq tag libraries TAG were prepared for reading out the multiseq tags. We provide the raw data .fastq files  processed data   both raw counts.tsv.gz and filtered by total UMI counts filtered.h5ad files and the entire filtered data post removing doublets as all data.h5ad. We also provide counts for multi seq tags example  TAG 1.counts.csv. Information about pooling libraries and library indices is provided in Pooling Samples.xlsx. Only 24 hpf data was used for Kukreja et. al. 2024 and hence the cell state information we provide in the all data.h5ad is only for 24 hpf.,,pubmed:37546736,,24  38 hpf and 48 hpf tails,GSM8328864,,source name:embryo tail|tissue:embryo tail|geo loc name:missing|collection date:missing,24  38 hpf and 48 hpf tails,"Reads were mapped onto the Zebrafish genome as described in Kukreja et al. 2024 manuscript. Multi seq barcodes for each sample were identified using a custom pipeline available here: https://github.com/AllonKleinLab/klunctions/. Barcode abundance was used to manually remove multiplet populations as well as assign cells to their appropriate sample. Data from only 24 hpf tails were used for the manuscript. We provide 8 FASTQ files 2 lanes x 4 reads per lane. The read files from an inDrops run have the following content: * R1 001.fastq.gz : contains the three prime UTR cDNA read * R2 001.fastq.gz : contains the first half of the cell barcode * R3 001.fastq.gz : contains the library index for demultiplexing libraries * R4 001.fastq.gz : contains the second half of the barcode and the UMI.  All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis github.com/indrops. Single cell transcriptomes were barcoded using inDrops Klein et al  Cell 2015. Standard transcriptome RNA seq libraries were processed as reported in Zilionis et al. Nature Protocol 2016 using inDrops v3 protocol. The transcriptome libraries were sequenced on reads Illumina NextSeq 500. Libraries used standard Illumina sequencing primers and 61 cycles for Read1  14 cycles for Read2  8 cycles each for IndexRead1 and IndexRead2. Raw fastq files was processed using inDrops.py pipeline github.com/indrops/indrops. Sequenced reads were mapped to a zebrafish reference transcriptome built from the zebrafish GRCz10 genome assembly Assembly Accession: GCF 000002035.5 using bowtie version 1.1.143. To obtain the final counts matrix used for data analysis  total count filters were applied as described in Kukreja et. al. 2024  method section ""Single cell RNA seq Data preprocessing"" Assembly: GRCz10 genome assembly Assembly Accession: GCF 000002035.5 Supplementary files format and content: Raw counts for transcriptome tsv.gz: cell barcode  gene names  and raw counts for all cells Supplementary files format and content: Raw counts for multi seq tags csv.gz: cell barcode  tag sequence  and raw counts for all cells Supplementary files format and content: Filtered barcodes filtered.h5ad: cell barcode  and associated metadata for all cells Library strategy: inDrops v3 scRNA seq",embryo tail,,Forty zebrafish tail samples collected at 24  38 hpf and 48 hpf  were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly  the tails were dissociated with a mixture of DNaseI 20µg/mL  Collagenase/Dispase 8 mg/mL  and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled  washed with 1% BSA + PBS  and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.,,tissue:embryo tail,GSM8328864,GSM8328864: 24  38 hpf and 48 hpf tails; Danio rerio; OTHER,GSM8328864 r1,GSM8328864,1,Forty zebrafish tail samples collected at 24  38 hpf and 48 hpf  were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly  the tails were dissociated with a mixture of DNaseI 20µg/mL  Collagenase/Dispase 8 mg/mL  and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled  washed with 1% BSA + PBS  and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP513930,,,Undetermined_S0_L002_R1_001.fastq.gz Undetermined_S0_L002_R2_001.fastq.gz Undetermined_S0_L002_R3_001.fastq.gz Undetermined_S0_L002_R4_001.fastq.gz,fastq fastq fastq fastq,58603546956.0,505202991.0,GSM8328864 r1,0:86 1:8 2:8 3:14,A:13191204330;C:9162028793;G:9431065581;T:11662090182;N:1068340,86,8,8,14,13191204330,9162028793,9431065581,11662090182,1068340,SRX24925451,SRS21630866,SRA1899240,Harvard University,Harvard University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,other,trueseq,sc,single_cell_droplet,indrops,,United States,2024-06-14,Multi-stage,Embryo,Tail,Multi-system
32782,SRR29411986,SRX24925451,SRS21630866,SRP513930,PRJNA1124008,Cell state transitions are decoupled from cell division during early embryo development [II],GSE269848,Other,Paper abstract: As tissues develop  cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation  we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. However  in the absence of cell division  differentiation slows down in some cell types  and cells exhibit global stress responses. While differentiation is robust to blocking cell division  the proportions of cells across cell states are not but show evidence of partial compensation. This work clarifies our understanding of the role of cell division in development and showcases the utility of combining embryo wide perturbations with single cell RNA sequencing to uncover the role of common biological processes across multiple tissues. Overall design: Design of experiment for this particular dataset: Forty tails from zebrafish embryos at 24  38 hpf and 48 hpf were collected. Cells were dissociated from these tails and multi seq tags were added to the cells for each time point. Cells from all time points were pooled and single cell sequencing was performed using Indrops. Four gene expression GEX libraries were prepared for transcriptomic information and four multiseq tag libraries TAG were prepared for reading out the multiseq tags. We provide the raw data .fastq files  processed data   both raw counts.tsv.gz and filtered by total UMI counts filtered.h5ad files and the entire filtered data post removing doublets as all data.h5ad. We also provide counts for multi seq tags example  TAG 1.counts.csv. Information about pooling libraries and library indices is provided in Pooling Samples.xlsx. Only 24 hpf data was used for Kukreja et. al. 2024 and hence the cell state information we provide in the all data.h5ad is only for 24 hpf.,,pubmed:37546736,,24  38 hpf and 48 hpf tails,GSM8328864,,source name:embryo tail|tissue:embryo tail|geo loc name:missing|collection date:missing,24  38 hpf and 48 hpf tails,"Reads were mapped onto the Zebrafish genome as described in Kukreja et al. 2024 manuscript. Multi seq barcodes for each sample were identified using a custom pipeline available here: https://github.com/AllonKleinLab/klunctions/. Barcode abundance was used to manually remove multiplet populations as well as assign cells to their appropriate sample. Data from only 24 hpf tails were used for the manuscript. We provide 8 FASTQ files 2 lanes x 4 reads per lane. The read files from an inDrops run have the following content: * R1 001.fastq.gz : contains the three prime UTR cDNA read * R2 001.fastq.gz : contains the first half of the cell barcode * R3 001.fastq.gz : contains the library index for demultiplexing libraries * R4 001.fastq.gz : contains the second half of the barcode and the UMI.  All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis github.com/indrops. Single cell transcriptomes were barcoded using inDrops Klein et al  Cell 2015. Standard transcriptome RNA seq libraries were processed as reported in Zilionis et al. Nature Protocol 2016 using inDrops v3 protocol. The transcriptome libraries were sequenced on reads Illumina NextSeq 500. Libraries used standard Illumina sequencing primers and 61 cycles for Read1  14 cycles for Read2  8 cycles each for IndexRead1 and IndexRead2. Raw fastq files was processed using inDrops.py pipeline github.com/indrops/indrops. Sequenced reads were mapped to a zebrafish reference transcriptome built from the zebrafish GRCz10 genome assembly Assembly Accession: GCF 000002035.5 using bowtie version 1.1.143. To obtain the final counts matrix used for data analysis  total count filters were applied as described in Kukreja et. al. 2024  method section ""Single cell RNA seq Data preprocessing"" Assembly: GRCz10 genome assembly Assembly Accession: GCF 000002035.5 Supplementary files format and content: Raw counts for transcriptome tsv.gz: cell barcode  gene names  and raw counts for all cells Supplementary files format and content: Raw counts for multi seq tags csv.gz: cell barcode  tag sequence  and raw counts for all cells Supplementary files format and content: Filtered barcodes filtered.h5ad: cell barcode  and associated metadata for all cells Library strategy: inDrops v3 scRNA seq",embryo tail,,Forty zebrafish tail samples collected at 24  38 hpf and 48 hpf  were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly  the tails were dissociated with a mixture of DNaseI 20µg/mL  Collagenase/Dispase 8 mg/mL  and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled  washed with 1% BSA + PBS  and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.,,tissue:embryo tail,GSM8328864,GSM8328864: 24  38 hpf and 48 hpf tails; Danio rerio; OTHER,GSM8328864 r1,GSM8328864,1,Forty zebrafish tail samples collected at 24  38 hpf and 48 hpf  were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly  the tails were dissociated with a mixture of DNaseI 20µg/mL  Collagenase/Dispase 8 mg/mL  and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled  washed with 1% BSA + PBS  and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP513930,,,Undetermined_S0_L001_R1_001.fastq.gz Undetermined_S0_L001_R2_001.fastq.gz Undetermined_S0_L001_R3_001.fastq.gz Undetermined_S0_L001_R4_001.fastq.gz,fastq fastq fastq fastq,44072422880.0,379934680.0,GSM8328864 r2,0:86 1:8 2:8 3:14,A:9919784228;C:6894965731;G:7094749745;T:8764100624;N:782152,86,8,8,14,9919784228,6894965731,7094749745,8764100624,782152,SRX24925451,SRS21630866,SRA1899240,Harvard University,Harvard University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,other,trueseq,sc,single_cell_droplet,indrops,,United States,2024-06-14,Multi-stage,Embryo,Tail,Multi-system
38049,SRR1519899,SRX657112,SRS662299,SRP044634,PRJNA255636,mRNA sequencing of embryonic tails of sih mutants at 28 hpf,GSE59563,Transcriptome Analysis,We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf,,,,sih3,GSM1439473,,tissue:tail derived cells|genotype/variation:sih|embryonic stage:28 hpf,sih3,Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id  Gene name and one column for each sample containing the normalized read counts,tail derived cells,sih embryos lack heart contraction,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,Embryos were grown in normal conditions,genotype/variation:sih|embryonic stage:28 hpf,GSM1439473,GSM1439473: sih3; Danio rerio; RNA Seq,GSM1439473,,1,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,GEO Accession:GSM1439473,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP044634,,,JGZ-06.fastq.gz,fastq,1416036978.0,26222907.0,GSM1439473 r1,0:54,A:342287675;C:370618836;G:361870457;T:341179934;N:80076,54,,,,342287675,370618836,361870457,341179934,80076,SRX657112,SRS662299,SRA175990,GEO,IGBMC,1,0.96217,,0.03055,,0.76869,,0.44925,,54,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2014-07-18,Pharyngula,Embryo,Tail,Multi-system
38050,SRR1519898,SRX657111,SRS662291,SRP044634,PRJNA255636,mRNA sequencing of embryonic tails of sih mutants at 28 hpf,GSE59563,Transcriptome Analysis,We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf,,,,WT3,GSM1439472,,tissue:tail derived cells|genotype/variation:WT|embryonic stage:28 hpf,WT3,Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id  Gene name and one column for each sample containing the normalized read counts,tail derived cells,sih embryos lack heart contraction,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,Embryos were grown in normal conditions,genotype/variation:WT|embryonic stage:28 hpf,GSM1439472,GSM1439472: WT3; Danio rerio; RNA Seq,GSM1439472,,1,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,GEO Accession:GSM1439472,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP044634,,,JGZ-05.fastq.gz,fastq,1787680692.0,33105198.0,GSM1439472 r1,0:54,A:442553431;C:457003567;G:446438405;T:441598672;N:86617,54,,,,442553431,457003567,446438405,441598672,86617,SRX657111,SRS662291,SRA175990,GEO,IGBMC,1,0.96318,,0.03918,,0.75371,,0.4423,,54,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2014-07-18,Pharyngula,Embryo,Tail,Multi-system
38051,SRR1519897,SRX657110,SRS662290,SRP044634,PRJNA255636,mRNA sequencing of embryonic tails of sih mutants at 28 hpf,GSE59563,Transcriptome Analysis,We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf,,,,sih2,GSM1439471,,tissue:tail derived cells|genotype/variation:sih|embryonic stage:28 hpf,sih2,Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id  Gene name and one column for each sample containing the normalized read counts,tail derived cells,sih embryos lack heart contraction,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,Embryos were grown in normal conditions,genotype/variation:sih|embryonic stage:28 hpf,GSM1439471,GSM1439471: sih2; Danio rerio; RNA Seq,GSM1439471,,1,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,GEO Accession:GSM1439471,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP044634,,,JGZ-04.fastq.gz,fastq,1813069386.0,33575359.0,GSM1439471 r1,0:54,A:462594376;C:449896725;G:440482879;T:460019095;N:76311,54,,,,462594376,449896725,440482879,460019095,76311,SRX657110,SRS662290,SRA175990,GEO,IGBMC,1,0.95859,,0.05282,,0.74199,,0.47244,,54,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2014-07-18,Pharyngula,Embryo,Tail,Multi-system
38052,SRR1519896,SRX657109,SRS662289,SRP044634,PRJNA255636,mRNA sequencing of embryonic tails of sih mutants at 28 hpf,GSE59563,Transcriptome Analysis,We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf,,,,WT2,GSM1439470,,tissue:tail derived cells|genotype/variation:WT|embryonic stage:28 hpf,WT2,Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id  Gene name and one column for each sample containing the normalized read counts,tail derived cells,sih embryos lack heart contraction,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,Embryos were grown in normal conditions,genotype/variation:WT|embryonic stage:28 hpf,GSM1439470,GSM1439470: WT2; Danio rerio; RNA Seq,GSM1439470,,1,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,GEO Accession:GSM1439470,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP044634,,,JGZ-03.fastq.gz,fastq,1866194316.0,34559154.0,GSM1439470 r1,0:54,A:483946414;C:453986455;G:443561481;T:484623941;N:76025,54,,,,483946414,453986455,443561481,484623941,76025,SRX657109,SRS662289,SRA175990,GEO,IGBMC,1,0.95615,,0.06195,,0.73594,,0.47144,,54,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2014-07-18,Pharyngula,Embryo,Tail,Multi-system
38053,SRR1519895,SRX657108,SRS662288,SRP044634,PRJNA255636,mRNA sequencing of embryonic tails of sih mutants at 28 hpf,GSE59563,Transcriptome Analysis,We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf,,,,sih1,GSM1439469,,tissue:tail derived cells|genotype/variation:sih|embryonic stage:28 hpf,sih1,Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id  Gene name and one column for each sample containing the normalized read counts,tail derived cells,sih embryos lack heart contraction,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,Embryos were grown in normal conditions,genotype/variation:sih|embryonic stage:28 hpf,GSM1439469,GSM1439469: sih1; Danio rerio; RNA Seq,GSM1439469,,1,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,GEO Accession:GSM1439469,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP044634,,,JGZ-02.fastq.gz,fastq,1451212470.0,26874305.0,GSM1439469 r1,0:54,A:368354355;C:360129390;G:353350795;T:369317437;N:60493,54,,,,368354355,360129390,353350795,369317437,60493,SRX657108,SRS662288,SRA175990,GEO,IGBMC,1,0.94911,,0.04509,,0.74604,,0.46107,,54,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2014-07-18,Pharyngula,Embryo,Tail,Multi-system
38054,SRR1519894,SRX657107,SRS662287,SRP044634,PRJNA255636,mRNA sequencing of embryonic tails of sih mutants at 28 hpf,GSE59563,Transcriptome Analysis,We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf,,,,WT1,GSM1439468,,tissue:tail derived cells|genotype/variation:WT|embryonic stage:28 hpf,WT1,Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id  Gene name and one column for each sample containing the normalized read counts,tail derived cells,sih embryos lack heart contraction,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,Embryos were grown in normal conditions,genotype/variation:WT|embryonic stage:28 hpf,GSM1439468,GSM1439468: WT1; Danio rerio; RNA Seq,GSM1439468,,1,RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C  30 sec at 60°C  30 sec at 72°C] x 13 cycles; 5 min at 72°C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.,GEO Accession:GSM1439468,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP044634,,,JGZ-01.fastq.gz,fastq,1583485146.0,29323799.0,GSM1439468 r1,0:54,A:405051413;C:391145102;G:382645289;T:404569188;N:74154,54,,,,405051413,391145102,382645289,404569188,74154,SRX657107,SRS662287,SRA175990,GEO,IGBMC,1,0.94743,,0.05464,,0.73156,,0.46572,,54,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2014-07-18,Pharyngula,Embryo,Tail,Multi-system
41312,SRR4199307,SRX2148087,SRS1679265,SRP087617,PRJNA342262,Proliferation independent regulation of organ size by Notch signaling,GSE86571,Transcriptome Analysis,Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow  we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails  with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate  using HiSeq 2500 Illumina.,,pubmed:28085667,,NICD rep3,GSM2306087,,source name:dissociated embryo tails|strain:TgcldnB:GFP; TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf,NICD rep3,Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters  p 8   transcriptome index  G  o   no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters  p 4  g  o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters  m intersection nonempty  s no  f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample  one includes FPKM values for each Sample.,dissociated embryo tails,Zebrafish embryos positive for GFP were selected.,Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.,Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.,strain:TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf,GSM2306087,GSM2306087: NICD rep3; Danio rerio; RNA Seq,GSM2306087,,1,Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2306087,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP087617,,,mutant3.fastq.gz,fastq,1706861931.0,33467881.0,GSM2306087 r1,0:51 1:0,A:400027681;C:444926525;G:399939257;T:461913972;N:54496,51,0,,,400027681,444926525,399939257,461913972,54496,SRX2148087,SRS1679265,SRA464955,GEO,Stowers Institute for Medical Research,1,0.75848,,0.06958,,0.73616,,0.47901,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2016-09-08,Pharyngula,Embryo,Tail,Multi-system
41313,SRR4199306,SRX2148086,SRS1679264,SRP087617,PRJNA342262,Proliferation independent regulation of organ size by Notch signaling,GSE86571,Transcriptome Analysis,Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow  we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails  with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate  using HiSeq 2500 Illumina.,,pubmed:28085667,,NICD rep2,GSM2306086,,source name:dissociated embryo tails|strain:TgcldnB:GFP; TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf,NICD rep2,Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters  p 8   transcriptome index  G  o   no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters  p 4  g  o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters  m intersection nonempty  s no  f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample  one includes FPKM values for each Sample.,dissociated embryo tails,Zebrafish embryos positive for GFP were selected.,Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.,Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.,strain:TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf,GSM2306086,GSM2306086: NICD rep2; Danio rerio; RNA Seq,GSM2306086,,1,Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2306086,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP087617,,,mutant2.fastq.gz,fastq,1745551857.0,34226507.0,GSM2306086 r1,0:51 1:0,A:414724753;C:449494336;G:403529006;T:477747391;N:56371,51,0,,,414724753,449494336,403529006,477747391,56371,SRX2148086,SRS1679264,SRA464955,GEO,Stowers Institute for Medical Research,1,0.77355,,0.08842,,0.71674,,0.48589,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2016-09-08,Pharyngula,Embryo,Tail,Multi-system