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
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
63865,SRR14143478,SRX10512841,SRS8636598,SRP313475,PRJNA719789,scRNA seq of tailbud development in zebrafish,GSE171482,Other,We have performed single cell RNA seq of whole tailbuds in WT zebrafish at 16 hpf. Overall design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.,,,,Tailbud single cells at 16 hpf,GSM5226215,,source name:Dissociated tailbuds from 30 hpf 16 hpf embryos|transgenic:AB wildtypes|age:16 hpf embryo|tissue:dissociated tailbuds,Tailbud single cells at 16 hpf,FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: .csv file contains counts matrix for each cell that met quality thresholds,Dissociated tailbuds from 30 hpf 16 hpf embryos,,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. Linraries used 10X Chromiium chemistry v2 except Sample 7  which used chemistry v3,,transgenic:AB wildtypes|age:16 hpf embryo|tissue:dissociated tailbuds,GSM5226215,GSM5226215: Tailbud single cells at 16 hpf; Danio rerio; RNA Seq,GSM5226215,,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. Linraries used 10X Chromiium chemistry v2 except Sample 7  which used chemistry v3,GEO Accession:GSM5226215,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP313475,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=WT tailbud S1 L003 I1 001.fastq.gz   read2PairFiles=WT tailbud S1 L003 R1 001.fastq.gz   read3PairFiles=WT tailbud S1 L003 R2 001.fastq.gz,,,31286394882.0,246349566.0,GSM5226215 r1,0:8 1:28 2:91,A:8483875403;C:6562544452;G:7703313223;T:8535328683;N:1333121,8,28,91,,8483875403,6562544452,7703313223,8535328683,1333121,SRX10512841,SRS8636598,SRA1215249,GEO,"Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine",1,0.94915,,0.12419,,0.79411,,0.48155,,91,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-04-05,Segmentation,Embryo,Tail,Multi-system
63866,SRR14143479,SRX10512841,SRS8636598,SRP313475,PRJNA719789,scRNA seq of tailbud development in zebrafish,GSE171482,Other,We have performed single cell RNA seq of whole tailbuds in WT zebrafish at 16 hpf. Overall design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.,,,,Tailbud single cells at 16 hpf,GSM5226215,,source name:Dissociated tailbuds from 30 hpf 16 hpf embryos|transgenic:AB wildtypes|age:16 hpf embryo|tissue:dissociated tailbuds,Tailbud single cells at 16 hpf,FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: .csv file contains counts matrix for each cell that met quality thresholds,Dissociated tailbuds from 30 hpf 16 hpf embryos,,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. Linraries used 10X Chromiium chemistry v2 except Sample 7  which used chemistry v3,,transgenic:AB wildtypes|age:16 hpf embryo|tissue:dissociated tailbuds,GSM5226215,GSM5226215: Tailbud single cells at 16 hpf; Danio rerio; RNA Seq,GSM5226215,,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. Linraries used 10X Chromiium chemistry v2 except Sample 7  which used chemistry v3,GEO Accession:GSM5226215,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP313475,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=WT tailbud S2 L003 I1 001.fastq.gz   read2PairFiles=WT tailbud S2 L003 R1 001.fastq.gz   read3PairFiles=WT tailbud S2 L003 R2 001.fastq.gz,WT_tailbud_S2_L003_I1_001.fastq.gz WT_tailbud_S2_L003_R1_001.fastq.gz WT_tailbud_S2_L003_R2_001.fastq.gz,fastq fastq fastq,34222167268.0,269465884.0,GSM5226215 r2,0:8 1:28 2:91,A:10380791879;C:7173180527;G:7598116520;T:9068620061;N:1458281,8,28,91,,10380791879,7173180527,7598116520,9068620061,1458281,SRX10512841,SRS8636598,SRA1215249,GEO,"Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine",1,0.94862,,0.1236,,0.79322,,0.50153,,91,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-04-05,Segmentation,Embryo,Tail,Multi-system
63867,SRR14143480,SRX10512841,SRS8636598,SRP313475,PRJNA719789,scRNA seq of tailbud development in zebrafish,GSE171482,Other,We have performed single cell RNA seq of whole tailbuds in WT zebrafish at 16 hpf. Overall design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.,,,,Tailbud single cells at 16 hpf,GSM5226215,,source name:Dissociated tailbuds from 30 hpf 16 hpf embryos|transgenic:AB wildtypes|age:16 hpf embryo|tissue:dissociated tailbuds,Tailbud single cells at 16 hpf,FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: .csv file contains counts matrix for each cell that met quality thresholds,Dissociated tailbuds from 30 hpf 16 hpf embryos,,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. Linraries used 10X Chromiium chemistry v2 except Sample 7  which used chemistry v3,,transgenic:AB wildtypes|age:16 hpf embryo|tissue:dissociated tailbuds,GSM5226215,GSM5226215: Tailbud single cells at 16 hpf; Danio rerio; RNA Seq,GSM5226215,,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. Linraries used 10X Chromiium chemistry v2 except Sample 7  which used chemistry v3,GEO Accession:GSM5226215,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP313475,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=WT tailbud S3 L003 I1 001.fastq.gz   read2PairFiles=WT tailbud S3 L003 R1 001.fastq.gz   read3PairFiles=WT tailbud S3 L003 R2 001.fastq.gz,WT_tailbud_S3_L003_I1_001.fastq.gz WT_tailbud_S3_L003_R1_001.fastq.gz WT_tailbud_S3_L003_R2_001.fastq.gz,fastq fastq fastq,33676411438.0,265168594.0,GSM5226215 r3,0:8 1:28 2:91,A:9145545141;C:7581198882;G:7228819079;T:9719412772;N:1435564,8,28,91,,9145545141,7581198882,7228819079,9719412772,1435564,SRX10512841,SRS8636598,SRA1215249,GEO,"Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine",1,0.94728,,0.12372,,0.79366,,0.49386,,91,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-04-05,Segmentation,Embryo,Tail,Multi-system
63868,SRR14143481,SRX10512841,SRS8636598,SRP313475,PRJNA719789,scRNA seq of tailbud development in zebrafish,GSE171482,Other,We have performed single cell RNA seq of whole tailbuds in WT zebrafish at 16 hpf. Overall design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.,,,,Tailbud single cells at 16 hpf,GSM5226215,,source name:Dissociated tailbuds from 30 hpf 16 hpf embryos|transgenic:AB wildtypes|age:16 hpf embryo|tissue:dissociated tailbuds,Tailbud single cells at 16 hpf,FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: .csv file contains counts matrix for each cell that met quality thresholds,Dissociated tailbuds from 30 hpf 16 hpf embryos,,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. Linraries used 10X Chromiium chemistry v2 except Sample 7  which used chemistry v3,,transgenic:AB wildtypes|age:16 hpf embryo|tissue:dissociated tailbuds,GSM5226215,GSM5226215: Tailbud single cells at 16 hpf; Danio rerio; RNA Seq,GSM5226215,,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. Linraries used 10X Chromiium chemistry v2 except Sample 7  which used chemistry v3,GEO Accession:GSM5226215,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP313475,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=WT tailbud S4 L003 I1 001.fastq.gz   read2PairFiles=WT tailbud S4 L003 R1 001.fastq.gz   read3PairFiles=WT tailbud S4 L003 R2 001.fastq.gz,WT_tailbud_S4_L003_I1_001.fastq.gz WT_tailbud_S4_L003_R1_001.fastq.gz WT_tailbud_S4_L003_R2_001.fastq.gz,fastq fastq fastq,30944524598.0,243657674.0,GSM5226215 r4,0:8 1:28 2:91,A:8382983101;C:6979019830;G:7383731031;T:8197465285;N:1325351,8,28,91,,8382983101,6979019830,7383731031,8197465285,1325351,SRX10512841,SRS8636598,SRA1215249,GEO,"Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine",1,0.94927,,0.12443,,0.79316,,0.48307,,91,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-04-05,Segmentation,Embryo,Tail,Multi-system
64263,SRR14428602,SRX10779739,SRS8866172,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of notum 1 treatment embryo replicate 4,GSM5282506,,tissue:tail|treatment:notum 1,scRNA seq of notum 1 treatment embryo replicate 4,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:notum 1,GSM5282506,GSM5282506: scRNA seq of notum 1 treatment embryo replicate 4; Danio rerio; RNA Seq,GSM5282506,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282506,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,,WNT_MG2_S40_L006_R1_001.fastq.gz WNT_MG2_S40_L006_R2_001.fastq.gz,fastq fastq,59309016800.0,296545084.0,GSM5282506 r1,0:100 1:100,A:13101652467;C:9053865386;G:9914199388;T:27226829088;N:12470471,100,100,,,13101652467,9053865386,9914199388,27226829088,12470471,SRX10779739,SRS8866172,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",2,0.00907,0.91374,0.00232,0.07221,0.99293,0.82822,0.5,0.50749,100,100,T,B,mate1 technical by mapping diff,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64264,SRR14428601,SRX10779738,SRS8866171,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of notum 1 treatment embryo replicate 3,GSM5282505,,tissue:tail|treatment:notum 1,scRNA seq of notum 1 treatment embryo replicate 3,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:notum 1,GSM5282505,GSM5282505: scRNA seq of notum 1 treatment embryo replicate 3; Danio rerio; RNA Seq,GSM5282505,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282505,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,,WNT_MG1_S39_L005_R1_001.fastq.gz WNT_MG1_S39_L005_R2_001.fastq.gz,fastq fastq,75003307800.0,375016539.0,GSM5282505 r1,0:100 1:100,A:17011122660;C:12505646501;G:12322737410;T:33144126985;N:19674244,100,100,,,17011122660,12505646501,12322737410,33144126985,19674244,SRX10779738,SRS8866171,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",2,0.0068,0.94221,0.00175,0.08258,0.99608,0.82473,0.49289,0.52202,100,100,T,B,mate1 technical by mapping diff,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64265,SRR14428600,SRX10779737,SRS8866170,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of notum 1 treatment embryo replicate 2,GSM5282504,,tissue:tail|treatment:notum 1,scRNA seq of notum 1 treatment embryo replicate 2,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:notum 1,GSM5282504,GSM5282504: scRNA seq of notum 1 treatment embryo replicate 2; Danio rerio; RNA Seq,GSM5282504,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282504,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,,WNT_DJ2_S42_L008_R1_001.fastq.gz WNT_DJ2_S42_L008_R2_001.fastq.gz,fastq fastq,73921649200.0,369608246.0,GSM5282504 r1,0:100 1:100,A:16691509262;C:12147679273;G:12179457462;T:32881202116;N:21801087,100,100,,,16691509262,12147679273,12179457462,32881202116,21801087,SRX10779737,SRS8866170,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",2,0.00683,0.92595,0.00109,0.08047,0.99531,0.82558,0.5017,0.48675,100,100,T,B,mate1 technical by mapping diff,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64266,SRR14428599,SRX10779736,SRS8866169,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of notum 1 treatment embryo replicate 1,GSM5282503,,tissue:tail|treatment:notum 1,scRNA seq of notum 1 treatment embryo replicate 1,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:notum 1,GSM5282503,GSM5282503: scRNA seq of notum 1 treatment embryo replicate 1; Danio rerio; RNA Seq,GSM5282503,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282503,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,,WNT_DJ1_S41_L007_R1_001.fastq.gz WNT_DJ1_S41_L007_R2_001.fastq.gz,fastq fastq,72873756000.0,364368780.0,GSM5282503 r1,0:100 1:100,A:16621508845;C:12254073814;G:11510875104;T:32473791832;N:13506405,100,100,,,16621508845,12254073814,11510875104,32473791832,13506405,SRX10779736,SRS8866169,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",2,0.00358,0.94302,0.0008,0.08218,0.99803,0.82181,0.50485,0.51251,100,100,T,B,mate1 technical by mapping diff,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64267,SRR14428593,SRX10779735,SRS8866168,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of SU5402 treatment embryo replicate 4,GSM5282502,,tissue:tail|treatment:SU5402,scRNA seq of  SU5402 treatment embryo replicate 4,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:SU5402,GSM5282502,GSM5282502: scRNA seq of  SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq,GSM5282502,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282502,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SU4 DRT S2 L001 I1 001.fastq.gz   read2PairFiles=SU4 DRT S2 L001 R1 001.fastq.gz   read3PairFiles=SU4 DRT S2 L001 R2 001.fastq.gz,SU4_DRT_S2_L001_I1_001.fastq.gz SU4_DRT_S2_L001_R1_001.fastq.gz SU4_DRT_S2_L001_R2_001.fastq.gz,fastq fastq fastq,6902983527.0,54354201.0,GSM5282502 r1,0:8 1:28 2:91,A:1904129671;C:1528133826;G:1597676497;T:1870308784;N:2734749,8,28,91,,1904129671,1528133826,1597676497,1870308784,2734749,SRX10779735,SRS8866168,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93834,,0.14712,,0.80097,,0.53464,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64268,SRR14428594,SRX10779735,SRS8866168,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of SU5402 treatment embryo replicate 4,GSM5282502,,tissue:tail|treatment:SU5402,scRNA seq of  SU5402 treatment embryo replicate 4,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:SU5402,GSM5282502,GSM5282502: scRNA seq of  SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq,GSM5282502,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282502,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SU4 DRT S2 L002 I1 001.fastq.gz   read2PairFiles=SU4 DRT S2 L002 R1 001.fastq.gz   read3PairFiles=SU4 DRT S2 L002 R2 001.fastq.gz,SU4_DRT_S2_L002_I1_001.fastq.gz SU4_DRT_S2_L002_R1_001.fastq.gz SU4_DRT_S2_L002_R2_001.fastq.gz,fastq fastq fastq,7355984272.0,57921136.0,GSM5282502 r2,0:8 1:28 2:91,A:2029150464;C:1629831151;G:1703134376;T:1991639472;N:2228809,8,28,91,,2029150464,1629831151,1703134376,1991639472,2228809,SRX10779735,SRS8866168,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93751,,0.14654,,0.80048,,0.53568,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64269,SRR14428595,SRX10779735,SRS8866168,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of SU5402 treatment embryo replicate 4,GSM5282502,,tissue:tail|treatment:SU5402,scRNA seq of  SU5402 treatment embryo replicate 4,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:SU5402,GSM5282502,GSM5282502: scRNA seq of  SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq,GSM5282502,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282502,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SU4 DRT S2 L003 I1 001.fastq.gz   read2PairFiles=SU4 DRT S2 L003 R1 001.fastq.gz   read3PairFiles=SU4 DRT S2 L003 R2 001.fastq.gz,SU4_DRT_S2_L003_I1_001.fastq.gz SU4_DRT_S2_L003_R1_001.fastq.gz SU4_DRT_S2_L003_R2_001.fastq.gz,fastq fastq fastq,6915051321.0,54449223.0,GSM5282502 r3,0:8 1:28 2:91,A:1907859125;C:1531399983;G:1600723047;T:1872767703;N:2301463,8,28,91,,1907859125,1531399983,1600723047,1872767703,2301463,SRX10779735,SRS8866168,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93859,,0.14759,,0.80075,,0.53726,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64270,SRR14428596,SRX10779735,SRS8866168,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of SU5402 treatment embryo replicate 4,GSM5282502,,tissue:tail|treatment:SU5402,scRNA seq of  SU5402 treatment embryo replicate 4,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:SU5402,GSM5282502,GSM5282502: scRNA seq of  SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq,GSM5282502,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282502,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SU4 DRT S2 L004 I1 001.fastq.gz   read2PairFiles=SU4 DRT S2 L004 R1 001.fastq.gz   read3PairFiles=SU4 DRT S2 L004 R2 001.fastq.gz,SU4_DRT_S2_L004_I1_001.fastq.gz SU4_DRT_S2_L004_R1_001.fastq.gz SU4_DRT_S2_L004_R2_001.fastq.gz,fastq fastq fastq,6496116929.0,51150527.0,GSM5282502 r4,0:8 1:28 2:91,A:1791207713;C:1438082538;G:1503927125;T:1760463486;N:2436067,8,28,91,,1791207713,1438082538,1503927125,1760463486,2436067,SRX10779735,SRS8866168,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93855,,0.14517,,0.80142,,0.51836,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64271,SRR14428597,SRX10779735,SRS8866168,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of SU5402 treatment embryo replicate 4,GSM5282502,,tissue:tail|treatment:SU5402,scRNA seq of  SU5402 treatment embryo replicate 4,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:SU5402,GSM5282502,GSM5282502: scRNA seq of  SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq,GSM5282502,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282502,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SU4 DRT S2 L005 I1 001.fastq.gz   read2PairFiles=SU4 DRT S2 L005 R1 001.fastq.gz   read3PairFiles=SU4 DRT S2 L005 R2 001.fastq.gz,SU4_DRT_S2_L005_I1_001.fastq.gz SU4_DRT_S2_L005_R1_001.fastq.gz SU4_DRT_S2_L005_R2_001.fastq.gz,fastq fastq fastq,6925225545.0,54529335.0,GSM5282502 r5,0:8 1:28 2:91,A:1908749610;C:1534337999;G:1604298047;T:1874791459;N:3048430,8,28,91,,1908749610,1534337999,1604298047,1874791459,3048430,SRX10779735,SRS8866168,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93705,,0.14527,,0.79811,,0.49961,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64272,SRR14428598,SRX10779735,SRS8866168,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of SU5402 treatment embryo replicate 4,GSM5282502,,tissue:tail|treatment:SU5402,scRNA seq of  SU5402 treatment embryo replicate 4,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:SU5402,GSM5282502,GSM5282502: scRNA seq of  SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq,GSM5282502,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282502,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SU4 DRT S2 L006 I1 001.fastq.gz   read2PairFiles=SU4 DRT S2 L006 R1 001.fastq.gz   read3PairFiles=SU4 DRT S2 L006 R2 001.fastq.gz,SU4_DRT_S2_L006_I1_001.fastq.gz SU4_DRT_S2_L006_R1_001.fastq.gz SU4_DRT_S2_L006_R2_001.fastq.gz,fastq fastq fastq,5772764553.0,45454839.0,GSM5282502 r6,0:8 1:28 2:91,A:1592079310;C:1277414314;G:1335013911;T:1565676607;N:2580411,8,28,91,,1592079310,1277414314,1335013911,1565676607,2580411,SRX10779735,SRS8866168,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93895,,0.1477,,0.79772,,0.52786,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64273,SRR14428587,SRX10779734,SRS8866167,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of SU5402 treatment embryo replicate 3,GSM5282501,,tissue:tail|treatment:SU5402,scRNA seq of  SU5402 treatment embryo replicate 3,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:SU5402,GSM5282501,GSM5282501: scRNA seq of  SU5402 treatment embryo replicate 3; Danio rerio; RNA Seq,GSM5282501,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282501,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SU3 DRT S1 L001 I1 001.fastq.gz   read2PairFiles=SU3 DRT S1 L001 R1 001.fastq.gz   read3PairFiles=SU3 DRT S1 L001 R2 001.fastq.gz,SU3_DRT_S1_L001_I1_001.fastq.gz SU3_DRT_S1_L001_R1_001.fastq.gz SU3_DRT_S1_L001_R2_001.fastq.gz,fastq fastq fastq,8251078748.0,64969124.0,GSM5282501 r1,0:8 1:28 2:91,A:2304710369;C:1797342936;G:1900704244;T:2245059790;N:3261409,8,28,91,,2304710369,1797342936,1900704244,2245059790,3261409,SRX10779734,SRS8866167,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92754,,0.16532,,0.81462,,0.52604,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64274,SRR14428588,SRX10779734,SRS8866167,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of SU5402 treatment embryo replicate 3,GSM5282501,,tissue:tail|treatment:SU5402,scRNA seq of  SU5402 treatment embryo replicate 3,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:SU5402,GSM5282501,GSM5282501: scRNA seq of  SU5402 treatment embryo replicate 3; Danio rerio; RNA Seq,GSM5282501,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282501,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SU3 DRT S1 L002 I1 001.fastq.gz   read2PairFiles=SU3 DRT S1 L002 R1 001.fastq.gz   read3PairFiles=SU3 DRT S1 L002 R2 001.fastq.gz,SU3_DRT_S1_L002_I1_001.fastq.gz SU3_DRT_S1_L002_R1_001.fastq.gz SU3_DRT_S1_L002_R2_001.fastq.gz,fastq fastq fastq,8745931073.0,68865599.0,GSM5282501 r2,0:8 1:28 2:91,A:2444384848;C:1906587775;G:2015145654;T:2377159417;N:2653379,8,28,91,,2444384848,1906587775,2015145654,2377159417,2653379,SRX10779734,SRS8866167,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92881,,0.16592,,0.8132,,0.53153,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64275,SRR14428589,SRX10779734,SRS8866167,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of SU5402 treatment embryo replicate 3,GSM5282501,,tissue:tail|treatment:SU5402,scRNA seq of  SU5402 treatment embryo replicate 3,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:SU5402,GSM5282501,GSM5282501: scRNA seq of  SU5402 treatment embryo replicate 3; Danio rerio; RNA Seq,GSM5282501,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282501,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SU3 DRT S1 L003 I1 001.fastq.gz   read2PairFiles=SU3 DRT S1 L003 R1 001.fastq.gz   read3PairFiles=SU3 DRT S1 L003 R2 001.fastq.gz,SU3_DRT_S1_L003_I1_001.fastq.gz SU3_DRT_S1_L003_R1_001.fastq.gz SU3_DRT_S1_L003_R2_001.fastq.gz,fastq fastq fastq,8264591040.0,65075520.0,GSM5282501 r3,0:8 1:28 2:91,A:2309308717;C:1801010847;G:1903956632;T:2247562936;N:2751908,8,28,91,,2309308717,1801010847,1903956632,2247562936,2751908,SRX10779734,SRS8866167,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92814,,0.16403,,0.81186,,0.54282,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64276,SRR14428590,SRX10779734,SRS8866167,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of SU5402 treatment embryo replicate 3,GSM5282501,,tissue:tail|treatment:SU5402,scRNA seq of  SU5402 treatment embryo replicate 3,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:SU5402,GSM5282501,GSM5282501: scRNA seq of  SU5402 treatment embryo replicate 3; Danio rerio; RNA Seq,GSM5282501,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282501,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SU3 DRT S1 L004 I1 001.fastq.gz   read2PairFiles=SU3 DRT S1 L004 R1 001.fastq.gz   read3PairFiles=SU3 DRT S1 L004 R2 001.fastq.gz,SU3_DRT_S1_L004_I1_001.fastq.gz SU3_DRT_S1_L004_R1_001.fastq.gz SU3_DRT_S1_L004_R2_001.fastq.gz,fastq fastq fastq,7798248691.0,61403533.0,GSM5282501 r4,0:8 1:28 2:91,A:2174880077;C:1699441539;G:1797168334;T:2123840121;N:2918620,8,28,91,,2174880077,1699441539,1797168334,2123840121,2918620,SRX10779734,SRS8866167,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92897,,0.16544,,0.81138,,0.53674,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64277,SRR14428591,SRX10779734,SRS8866167,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of SU5402 treatment embryo replicate 3,GSM5282501,,tissue:tail|treatment:SU5402,scRNA seq of  SU5402 treatment embryo replicate 3,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:SU5402,GSM5282501,GSM5282501: scRNA seq of  SU5402 treatment embryo replicate 3; Danio rerio; RNA Seq,GSM5282501,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282501,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SU3 DRT S1 L005 I1 001.fastq.gz   read2PairFiles=SU3 DRT S1 L005 R1 001.fastq.gz   read3PairFiles=SU3 DRT S1 L005 R2 001.fastq.gz,SU3_DRT_S1_L005_I1_001.fastq.gz SU3_DRT_S1_L005_R1_001.fastq.gz SU3_DRT_S1_L005_R2_001.fastq.gz,fastq fastq fastq,8288550733.0,65264179.0,GSM5282501 r5,0:8 1:28 2:91,A:2310828872;C:1807789428;G:1911417463;T:2254867256;N:3647714,8,28,91,,2310828872,1807789428,1911417463,2254867256,3647714,SRX10779734,SRS8866167,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92759,,0.1633,,0.81081,,0.51359,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64278,SRR14428592,SRX10779734,SRS8866167,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of SU5402 treatment embryo replicate 3,GSM5282501,,tissue:tail|treatment:SU5402,scRNA seq of  SU5402 treatment embryo replicate 3,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:SU5402,GSM5282501,GSM5282501: scRNA seq of  SU5402 treatment embryo replicate 3; Danio rerio; RNA Seq,GSM5282501,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282501,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SU3 DRT S1 L006 I1 001.fastq.gz   read2PairFiles=SU3 DRT S1 L006 R1 001.fastq.gz   read3PairFiles=SU3 DRT S1 L006 R2 001.fastq.gz,SU3_DRT_S1_L006_I1_001.fastq.gz SU3_DRT_S1_L006_R1_001.fastq.gz SU3_DRT_S1_L006_R2_001.fastq.gz,fastq fastq fastq,6973058063.0,54905969.0,GSM5282501 r6,0:8 1:28 2:91,A:1944153299;C:1519046931;G:1605222800;T:1901533624;N:3101409,8,28,91,,1944153299,1519046931,1605222800,1901533624,3101409,SRX10779734,SRS8866167,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92867,,0.16733,,0.81063,,0.54083,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64279,SRR14428585,SRX10779733,SRS8866166,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of SU5402 treatment embryo replicate 2,GSM5282500,,tissue:tail|treatment:SU5402,scRNA seq of  SU5402 treatment embryo replicate 2,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:SU5402,GSM5282500,GSM5282500: scRNA seq of  SU5402 treatment embryo replicate 2; Danio rerio; RNA Seq,GSM5282500,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282500,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SU2 DRT S2 L007 I1 001.fastq.gz   read2PairFiles=SU2 DRT S2 L007 R1 001.fastq.gz   read3PairFiles=SU2 DRT S2 L007 R2 001.fastq.gz,SU2_DRT_S2_L007_I1_001.fastq.gz SU2_DRT_S2_L007_R1_001.fastq.gz SU2_DRT_S2_L007_R2_001.fastq.gz,fastq fastq fastq,22706556822.0,178791786.0,GSM5282500 r1,0:8 1:28 2:91,A:6323509022;C:4887290384;G:5147542675;T:6339376387;N:8838354,8,28,91,,6323509022,4887290384,5147542675,6339376387,8838354,SRX10779733,SRS8866166,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92778,,0.13822,,0.79553,,0.51199,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64280,SRR14428586,SRX10779733,SRS8866166,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of SU5402 treatment embryo replicate 2,GSM5282500,,tissue:tail|treatment:SU5402,scRNA seq of  SU5402 treatment embryo replicate 2,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:SU5402,GSM5282500,GSM5282500: scRNA seq of  SU5402 treatment embryo replicate 2; Danio rerio; RNA Seq,GSM5282500,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282500,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SU2 DRT S2 L008 I1 001.fastq.gz   read2PairFiles=SU2 DRT S2 L008 R1 001.fastq.gz   read3PairFiles=SU2 DRT S2 L008 R2 001.fastq.gz,SU2_DRT_S2_L008_I1_001.fastq.gz SU2_DRT_S2_L008_R1_001.fastq.gz SU2_DRT_S2_L008_R2_001.fastq.gz,fastq fastq fastq,22610034790.0,178031770.0,GSM5282500 r2,0:8 1:28 2:91,A:6295049786;C:4863549001;G:5125752367;T:6316321559;N:9362077,8,28,91,,6295049786,4863549001,5125752367,6316321559,9362077,SRX10779733,SRS8866166,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92707,,0.13591,,0.79172,,0.53017,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64281,SRR14428583,SRX10779732,SRS8866165,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of SU5402 treatment embryo replicate 1,GSM5282499,,tissue:tail|treatment:SU5402,scRNA seq of  SU5402 treatment embryo replicate 1,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:SU5402,GSM5282499,GSM5282499: scRNA seq of  SU5402 treatment embryo replicate 1; Danio rerio; RNA Seq,GSM5282499,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282499,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SU1 DRT S1 L007 I1 001.fastq.gz   read2PairFiles=SU1 DRT S1 L007 R1 001.fastq.gz   read3PairFiles=SU1 DRT S1 L007 R2 001.fastq.gz,SU1_DRT_S1_L007_I1_001.fastq.gz SU1_DRT_S1_L007_R1_001.fastq.gz SU1_DRT_S1_L007_R2_001.fastq.gz,fastq fastq fastq,23249060436.0,183063468.0,GSM5282499 r1,0:8 1:28 2:91,A:6473687667;C:5003709390;G:5248540549;T:6514108143;N:9014687,8,28,91,,6473687667,5003709390,5248540549,6514108143,9014687,SRX10779732,SRS8866165,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92923,,0.129,,0.79864,,0.55507,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64282,SRR14428584,SRX10779732,SRS8866165,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of SU5402 treatment embryo replicate 1,GSM5282499,,tissue:tail|treatment:SU5402,scRNA seq of  SU5402 treatment embryo replicate 1,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:SU5402,GSM5282499,GSM5282499: scRNA seq of  SU5402 treatment embryo replicate 1; Danio rerio; RNA Seq,GSM5282499,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282499,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SU1 DRT S1 L008 I1 001.fastq.gz   read2PairFiles=SU1 DRT S1 L008 R1 001.fastq.gz   read3PairFiles=SU1 DRT S1 L008 R2 001.fastq.gz,SU1_DRT_S1_L008_I1_001.fastq.gz SU1_DRT_S1_L008_R1_001.fastq.gz SU1_DRT_S1_L008_R2_001.fastq.gz,fastq fastq fastq,23112024261.0,181984443.0,GSM5282499 r2,0:8 1:28 2:91,A:6437425883;C:4970144751;G:5217204284;T:6477722075;N:9527268,8,28,91,,6437425883,4970144751,5217204284,6477722075,9527268,SRX10779732,SRS8866165,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92795,,0.12824,,0.79707,,0.53168,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64283,SRR14428579,SRX10779731,SRS8866164,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of Wild type embryo replicate 4,GSM5282498,,tissue:tail|treatment:WT,scRNA seq of Wild type embryo replicate 4,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:WT,GSM5282498,GSM5282498: scRNA seq of Wild type embryo replicate 4; Danio rerio; RNA Seq,GSM5282498,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282498,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=MG2 DRT S3 L005 I1 001.fastq.gz   read2PairFiles=MG2 DRT S3 L005 R1 001.fastq.gz   read3PairFiles=MG2 DRT S3 L005 R2 001.fastq.gz,MG2_DRT_S3_L005_I1_001.fastq.gz MG2_DRT_S3_L005_R1_001.fastq.gz MG2_DRT_S3_L005_R2_001.fastq.gz,fastq fastq fastq,9492469966.0,74743858.0,GSM5282498 r1,0:8 1:28 2:91,A:2609486286;C:2069087738;G:2192904289;T:2617283463;N:3708190,8,28,91,,2609486286,2069087738,2192904289,2617283463,3708190,SRX10779731,SRS8866164,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92805,,0.11402,,0.80227,,0.48223,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64284,SRR14428580,SRX10779731,SRS8866164,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of Wild type embryo replicate 4,GSM5282498,,tissue:tail|treatment:WT,scRNA seq of Wild type embryo replicate 4,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:WT,GSM5282498,GSM5282498: scRNA seq of Wild type embryo replicate 4; Danio rerio; RNA Seq,GSM5282498,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282498,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=MG2 DRT S3 L006 I1 001.fastq.gz   read2PairFiles=MG2 DRT S3 L006 R1 001.fastq.gz   read3PairFiles=MG2 DRT S3 L006 R2 001.fastq.gz,MG2_DRT_S3_L006_I1_001.fastq.gz MG2_DRT_S3_L006_R1_001.fastq.gz MG2_DRT_S3_L006_R2_001.fastq.gz,fastq fastq fastq,9635960027.0,75873701.0,GSM5282498 r2,0:8 1:28 2:91,A:2647293422;C:2103232371;G:2225407295;T:2656262617;N:3764322,8,28,91,,2647293422,2103232371,2225407295,2656262617,3764322,SRX10779731,SRS8866164,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92692,,0.11501,,0.80403,,0.48189,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64285,SRR14428581,SRX10779731,SRS8866164,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of Wild type embryo replicate 4,GSM5282498,,tissue:tail|treatment:WT,scRNA seq of Wild type embryo replicate 4,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:WT,GSM5282498,GSM5282498: scRNA seq of Wild type embryo replicate 4; Danio rerio; RNA Seq,GSM5282498,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282498,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=MG2 DRT S3 L007 I1 001.fastq.gz   read2PairFiles=MG2 DRT S3 L007 R1 001.fastq.gz   read3PairFiles=MG2 DRT S3 L007 R2 001.fastq.gz,MG2_DRT_S3_L007_I1_001.fastq.gz MG2_DRT_S3_L007_R1_001.fastq.gz MG2_DRT_S3_L007_R2_001.fastq.gz,fastq fastq fastq,9387531390.0,73917570.0,GSM5282498 r3,0:8 1:28 2:91,A:2579905219;C:2047020899;G:2168062814;T:2588424779;N:4117679,8,28,91,,2579905219,2047020899,2168062814,2588424779,4117679,SRX10779731,SRS8866164,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92666,,0.11505,,0.80529,,0.49382,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64286,SRR14428582,SRX10779731,SRS8866164,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of Wild type embryo replicate 4,GSM5282498,,tissue:tail|treatment:WT,scRNA seq of Wild type embryo replicate 4,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:WT,GSM5282498,GSM5282498: scRNA seq of Wild type embryo replicate 4; Danio rerio; RNA Seq,GSM5282498,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282498,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=MG2 DRT S3 L008 I1 001.fastq.gz   read2PairFiles=MG2 DRT S3 L008 R1 001.fastq.gz   read3PairFiles=MG2 DRT S3 L008 R2 001.fastq.gz,MG2_DRT_S3_L008_I1_001.fastq.gz MG2_DRT_S3_L008_R1_001.fastq.gz MG2_DRT_S3_L008_R2_001.fastq.gz,fastq fastq fastq,9217689464.0,72580232.0,GSM5282498 r4,0:8 1:28 2:91,A:2533345035;C:2008536731;G:2129886197;T:2541165144;N:4756357,8,28,91,,2533345035,2008536731,2129886197,2541165144,4756357,SRX10779731,SRS8866164,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92286,,0.11529,,0.80395,,0.48636,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64287,SRR14428575,SRX10779730,SRS8866163,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of Wild type embryo replicate 3,GSM5282497,,tissue:tail|treatment:WT,scRNA seq of Wild type embryo replicate 3,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:WT,GSM5282497,GSM5282497: scRNA seq of Wild type embryo replicate 3; Danio rerio; RNA Seq,GSM5282497,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282497,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=MG1 DRT S2 L005 I1 001.fastq.gz   read2PairFiles=MG1 DRT S2 L005 R1 001.fastq.gz   read3PairFiles=MG1 DRT S2 L005 R2 001.fastq.gz,MG1_DRT_S2_L005_I1_001.fastq.gz MG1_DRT_S2_L005_R1_001.fastq.gz MG1_DRT_S2_L005_R2_001.fastq.gz,fastq fastq fastq,17349575664.0,136610832.0,GSM5282497 r1,0:8 1:28 2:91,A:4818340596;C:3752070379;G:3990473269;T:4781914390;N:6777030,8,28,91,,4818340596,3752070379,3990473269,4781914390,6777030,SRX10779730,SRS8866163,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.9284,,0.10948,,0.80547,,0.49189,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64288,SRR14428576,SRX10779730,SRS8866163,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of Wild type embryo replicate 3,GSM5282497,,tissue:tail|treatment:WT,scRNA seq of Wild type embryo replicate 3,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:WT,GSM5282497,GSM5282497: scRNA seq of Wild type embryo replicate 3; Danio rerio; RNA Seq,GSM5282497,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282497,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=MG1 DRT S2 L006 I1 001.fastq.gz   read2PairFiles=MG1 DRT S2 L006 R1 001.fastq.gz   read3PairFiles=MG1 DRT S2 L006 R2 001.fastq.gz,MG1_DRT_S2_L006_I1_001.fastq.gz MG1_DRT_S2_L006_R1_001.fastq.gz MG1_DRT_S2_L006_R2_001.fastq.gz,fastq fastq fastq,17618903294.0,138731522.0,GSM5282497 r2,0:8 1:28 2:91,A:4890473222;C:3815291120;G:4050726863;T:4855538370;N:6873719,8,28,91,,4890473222,3815291120,4050726863,4855538370,6873719,SRX10779730,SRS8866163,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92706,,0.1099,,0.80543,,0.49186,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64289,SRR14428577,SRX10779730,SRS8866163,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of Wild type embryo replicate 3,GSM5282497,,tissue:tail|treatment:WT,scRNA seq of Wild type embryo replicate 3,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:WT,GSM5282497,GSM5282497: scRNA seq of Wild type embryo replicate 3; Danio rerio; RNA Seq,GSM5282497,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282497,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=MG1 DRT S2 L007 I1 001.fastq.gz   read2PairFiles=MG1 DRT S2 L007 R1 001.fastq.gz   read3PairFiles=MG1 DRT S2 L007 R2 001.fastq.gz,MG1_DRT_S2_L007_I1_001.fastq.gz MG1_DRT_S2_L007_R1_001.fastq.gz MG1_DRT_S2_L007_R2_001.fastq.gz,fastq fastq fastq,17163315178.0,135144214.0,GSM5282497 r3,0:8 1:28 2:91,A:4766251435;C:3713084450;G:3945754157;T:4730698036;N:7527100,8,28,91,,4766251435,3713084450,3945754157,4730698036,7527100,SRX10779730,SRS8866163,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92754,,0.10835,,0.80797,,0.48866,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64290,SRR14428578,SRX10779730,SRS8866163,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of Wild type embryo replicate 3,GSM5282497,,tissue:tail|treatment:WT,scRNA seq of Wild type embryo replicate 3,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:WT,GSM5282497,GSM5282497: scRNA seq of Wild type embryo replicate 3; Danio rerio; RNA Seq,GSM5282497,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282497,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=MG1 DRT S2 L008 I1 001.fastq.gz   read2PairFiles=MG1 DRT S2 L008 R1 001.fastq.gz   read3PairFiles=MG1 DRT S2 L008 R2 001.fastq.gz,MG1_DRT_S2_L008_I1_001.fastq.gz MG1_DRT_S2_L008_R1_001.fastq.gz MG1_DRT_S2_L008_R2_001.fastq.gz,fastq fastq fastq,16809702347.0,132359861.0,GSM5282497 r4,0:8 1:28 2:91,A:4667371642;C:3633855882;G:3867101355;T:4632748337;N:8625131,8,28,91,,4667371642,3633855882,3867101355,4632748337,8625131,SRX10779730,SRS8866163,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92328,,0.10721,,0.80367,,0.47808,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64291,SRR14428569,SRX10779729,SRS8866162,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 4,GSM5282496,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 4,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282496,GSM5282496: scRNA seq of  DMH1 treatment embryo replicate 4; Danio rerio; RNA Seq,GSM5282496,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282496,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH4 DRT S6 L001 I1 001.fastq.gz   read2PairFiles=DMH4 DRT S6 L001 R1 001.fastq.gz   read3PairFiles=DMH4 DRT S6 L001 R2 001.fastq.gz,DMH4_DRT_S6_L001_I1_001.fastq.gz DMH4_DRT_S6_L001_R1_001.fastq.gz DMH4_DRT_S6_L001_R2_001.fastq.gz,fastq fastq fastq,7123207877.0,56088251.0,GSM5282496 r1,0:8 1:28 2:91,A:1962729920;C:1588676173;G:1649353500;T:1919637412;N:2810872,8,28,91,,1962729920,1588676173,1649353500,1919637412,2810872,SRX10779729,SRS8866162,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93588,,0.14896,,0.79758,,0.49446,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64292,SRR14428570,SRX10779729,SRS8866162,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 4,GSM5282496,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 4,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282496,GSM5282496: scRNA seq of  DMH1 treatment embryo replicate 4; Danio rerio; RNA Seq,GSM5282496,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282496,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH4 DRT S6 L002 I1 001.fastq.gz   read2PairFiles=DMH4 DRT S6 L002 R1 001.fastq.gz   read3PairFiles=DMH4 DRT S6 L002 R2 001.fastq.gz,DMH4_DRT_S6_L002_I1_001.fastq.gz DMH4_DRT_S6_L002_R1_001.fastq.gz DMH4_DRT_S6_L002_R2_001.fastq.gz,fastq fastq fastq,7586038422.0,59732586.0,GSM5282496 r2,0:8 1:28 2:91,A:2091122151;C:1693169697;G:1756654249;T:2042799697;N:2292628,8,28,91,,2091122151,1693169697,1756654249,2042799697,2292628,SRX10779729,SRS8866162,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93788,,0.15089,,0.79634,,0.5178,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64293,SRR14428571,SRX10779729,SRS8866162,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 4,GSM5282496,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 4,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282496,GSM5282496: scRNA seq of  DMH1 treatment embryo replicate 4; Danio rerio; RNA Seq,GSM5282496,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282496,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH4 DRT S6 L003 I1 001.fastq.gz   read2PairFiles=DMH4 DRT S6 L003 R1 001.fastq.gz   read3PairFiles=DMH4 DRT S6 L003 R2 001.fastq.gz,DMH4_DRT_S6_L003_I1_001.fastq.gz DMH4_DRT_S6_L003_R1_001.fastq.gz DMH4_DRT_S6_L003_R2_001.fastq.gz,fastq fastq fastq,7142674183.0,56241529.0,GSM5282496 r3,0:8 1:28 2:91,A:1968941716;C:1593511481;G:1653686658;T:1924167092;N:2367236,8,28,91,,1968941716,1593511481,1653686658,1924167092,2367236,SRX10779729,SRS8866162,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93752,,0.14955,,0.79644,,0.50838,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64294,SRR14428572,SRX10779729,SRS8866162,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 4,GSM5282496,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 4,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282496,GSM5282496: scRNA seq of  DMH1 treatment embryo replicate 4; Danio rerio; RNA Seq,GSM5282496,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282496,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH4 DRT S6 L004 I1 001.fastq.gz   read2PairFiles=DMH4 DRT S6 L004 R1 001.fastq.gz   read3PairFiles=DMH4 DRT S6 L004 R2 001.fastq.gz,DMH4_DRT_S6_L004_I1_001.fastq.gz DMH4_DRT_S6_L004_R1_001.fastq.gz DMH4_DRT_S6_L004_R2_001.fastq.gz,fastq fastq fastq,6713707045.0,52863835.0,GSM5282496 r4,0:8 1:28 2:91,A:1848906888;C:1497203954;G:1554812611;T:1810277268;N:2506324,8,28,91,,1848906888,1497203954,1554812611,1810277268,2506324,SRX10779729,SRS8866162,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93754,,0.1505,,0.79553,,0.52685,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64295,SRR14428573,SRX10779729,SRS8866162,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 4,GSM5282496,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 4,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282496,GSM5282496: scRNA seq of  DMH1 treatment embryo replicate 4; Danio rerio; RNA Seq,GSM5282496,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282496,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH4 DRT S6 L005 I1 001.fastq.gz   read2PairFiles=DMH4 DRT S6 L005 R1 001.fastq.gz   read3PairFiles=DMH4 DRT S6 L005 R2 001.fastq.gz,DMH4_DRT_S6_L005_I1_001.fastq.gz DMH4_DRT_S6_L005_R1_001.fastq.gz DMH4_DRT_S6_L005_R2_001.fastq.gz,fastq fastq fastq,7157753782.0,56360266.0,GSM5282496 r5,0:8 1:28 2:91,A:1970673839;C:1597733780;G:1658449707;T:1927756569;N:3139887,8,28,91,,1970673839,1597733780,1658449707,1927756569,3139887,SRX10779729,SRS8866162,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93636,,0.14837,,0.79545,,0.52489,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64296,SRR14428574,SRX10779729,SRS8866162,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 4,GSM5282496,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 4,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282496,GSM5282496: scRNA seq of  DMH1 treatment embryo replicate 4; Danio rerio; RNA Seq,GSM5282496,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282496,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH4 DRT S6 L006 I1 001.fastq.gz   read2PairFiles=DMH4 DRT S6 L006 R1 001.fastq.gz   read3PairFiles=DMH4 DRT S6 L006 R2 001.fastq.gz,DMH4_DRT_S6_L006_I1_001.fastq.gz DMH4_DRT_S6_L006_R1_001.fastq.gz DMH4_DRT_S6_L006_R2_001.fastq.gz,fastq fastq fastq,5969524129.0,47004127.0,GSM5282496 r6,0:8 1:28 2:91,A:1643952599;C:1330790681;G:1381135714;T:1610997620;N:2647515,8,28,91,,1643952599,1330790681,1381135714,1610997620,2647515,SRX10779729,SRS8866162,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93633,,0.15123,,0.7959,,0.5171,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64297,SRR14428563,SRX10779728,SRS8866161,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 3,GSM5282495,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 3,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282495,GSM5282495: scRNA seq of  DMH1 treatment embryo replicate 3; Danio rerio; RNA Seq,GSM5282495,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282495,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH3 DRT S5 L001 I1 001.fastq.gz   read2PairFiles=DMH3 DRT S5 L001 R1 001.fastq.gz   read3PairFiles=DMH3 DRT S5 L001 R2 001.fastq.gz,DMH3_DRT_S5_L001_I1_001.fastq.gz DMH3_DRT_S5_L001_R1_001.fastq.gz DMH3_DRT_S5_L001_R2_001.fastq.gz,fastq fastq fastq,7192416908.0,56633204.0,GSM5282495 r1,0:8 1:28 2:91,A:1991209107;C:1581442528;G:1671432113;T:1945488801;N:2844359,8,28,91,,1991209107,1581442528,1671432113,1945488801,2844359,SRX10779728,SRS8866161,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93559,,0.16137,,0.80133,,0.52562,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64298,SRR14428564,SRX10779728,SRS8866161,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 3,GSM5282495,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 3,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282495,GSM5282495: scRNA seq of  DMH1 treatment embryo replicate 3; Danio rerio; RNA Seq,GSM5282495,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282495,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH3 DRT S5 L002 I1 001.fastq.gz   read2PairFiles=DMH3 DRT S5 L002 R1 001.fastq.gz   read3PairFiles=DMH3 DRT S5 L002 R2 001.fastq.gz,DMH3_DRT_S5_L002_I1_001.fastq.gz DMH3_DRT_S5_L002_R1_001.fastq.gz DMH3_DRT_S5_L002_R2_001.fastq.gz,fastq fastq fastq,7657698553.0,60296839.0,GSM5282495 r2,0:8 1:28 2:91,A:2120078045;C:1685386017;G:1780204812;T:2069712107;N:2317572,8,28,91,,2120078045,1685386017,1780204812,2069712107,2317572,SRX10779728,SRS8866161,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93524,,0.16046,,0.80282,,0.53593,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64299,SRR14428565,SRX10779728,SRS8866161,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 3,GSM5282495,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 3,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282495,GSM5282495: scRNA seq of  DMH1 treatment embryo replicate 3; Danio rerio; RNA Seq,GSM5282495,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282495,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH3 DRT S5 L003 I1 001.fastq.gz   read2PairFiles=DMH3 DRT S5 L003 R1 001.fastq.gz   read3PairFiles=DMH3 DRT S5 L003 R2 001.fastq.gz,DMH3_DRT_S5_L003_I1_001.fastq.gz DMH3_DRT_S5_L003_R1_001.fastq.gz DMH3_DRT_S5_L003_R2_001.fastq.gz,fastq fastq fastq,7209380044.0,56766772.0,GSM5282495 r3,0:8 1:28 2:91,A:1996356430;C:1585660923;G:1675622569;T:1949346223;N:2393899,8,28,91,,1996356430,1585660923,1675622569,1949346223,2393899,SRX10779728,SRS8866161,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93589,,0.16061,,0.79896,,0.53735,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64300,SRR14428566,SRX10779728,SRS8866161,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 3,GSM5282495,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 3,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282495,GSM5282495: scRNA seq of  DMH1 treatment embryo replicate 3; Danio rerio; RNA Seq,GSM5282495,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282495,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH3 DRT S5 L004 I1 001.fastq.gz   read2PairFiles=DMH3 DRT S5 L004 R1 001.fastq.gz   read3PairFiles=DMH3 DRT S5 L004 R2 001.fastq.gz,DMH3_DRT_S5_L004_I1_001.fastq.gz DMH3_DRT_S5_L004_R1_001.fastq.gz DMH3_DRT_S5_L004_R2_001.fastq.gz,fastq fastq fastq,6776552233.0,53358679.0,GSM5282495 r4,0:8 1:28 2:91,A:1875578465;C:1489508714;G:1575289055;T:1833640279;N:2535720,8,28,91,,1875578465,1489508714,1575289055,1833640279,2535720,SRX10779728,SRS8866161,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93499,,0.16117,,0.79862,,0.55002,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64301,SRR14428567,SRX10779728,SRS8866161,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 3,GSM5282495,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 3,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282495,GSM5282495: scRNA seq of  DMH1 treatment embryo replicate 3; Danio rerio; RNA Seq,GSM5282495,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282495,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH3 DRT S5 L005 I1 001.fastq.gz   read2PairFiles=DMH3 DRT S5 L005 R1 001.fastq.gz   read3PairFiles=DMH3 DRT S5 L005 R2 001.fastq.gz,DMH3_DRT_S5_L005_R2_001.fastq.gz DMH3_DRT_S5_L005_R1_001.fastq.gz DMH3_DRT_S5_L005_I1_001.fastq.gz,fastq fastq fastq,7225366042.0,56892646.0,GSM5282495 r5,0:8 1:28 2:91,A:1998880759;C:1589714962;G:1680768850;T:1952828313;N:3173158,8,28,91,,1998880759,1589714962,1680768850,1952828313,3173158,SRX10779728,SRS8866161,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93582,,0.16069,,0.79876,,0.52951,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64302,SRR14428568,SRX10779728,SRS8866161,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 3,GSM5282495,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 3,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282495,GSM5282495: scRNA seq of  DMH1 treatment embryo replicate 3; Danio rerio; RNA Seq,GSM5282495,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282495,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH3 DRT S5 L006 I1 001.fastq.gz   read2PairFiles=DMH3 DRT S5 L006 R1 001.fastq.gz   read3PairFiles=DMH3 DRT S5 L006 R2 001.fastq.gz,DMH3_DRT_S5_L006_I1_001.fastq.gz DMH3_DRT_S5_L006_R1_001.fastq.gz DMH3_DRT_S5_L006_R2_001.fastq.gz,fastq fastq fastq,6030562234.0,47484742.0,GSM5282495 r6,0:8 1:28 2:91,A:1669516878;C:1324814074;G:1400296411;T:1633256111;N:2678760,8,28,91,,1669516878,1324814074,1400296411,1633256111,2678760,SRX10779728,SRS8866161,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93567,,0.16207,,0.79821,,0.54157,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64303,SRR14428557,SRX10779727,SRS8866160,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 2,GSM5282494,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 2,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282494,GSM5282494: scRNA seq of  DMH1 treatment embryo replicate 2; Danio rerio; RNA Seq,GSM5282494,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282494,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH2 DRT S4 L001 I1 001.fastq.gz   read2PairFiles=DMH2 DRT S4 L001 R1 001.fastq.gz   read3PairFiles=DMH2 DRT S4 L001 R2 001.fastq.gz,DMH2_DRT_S4_L001_I1_001.fastq.gz DMH2_DRT_S4_L001_R1_001.fastq.gz DMH2_DRT_S4_L001_R2_001.fastq.gz,fastq fastq fastq,6255378523.0,49254949.0,GSM5282494 r1,0:8 1:28 2:91,A:1738029934;C:1358217459;G:1451180213;T:1705471817;N:2479100,8,28,91,,1738029934,1358217459,1451180213,1705471817,2479100,SRX10779727,SRS8866160,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93582,,0.15096,,0.80066,,0.51934,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64304,SRR14428558,SRX10779727,SRS8866160,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 2,GSM5282494,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 2,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282494,GSM5282494: scRNA seq of  DMH1 treatment embryo replicate 2; Danio rerio; RNA Seq,GSM5282494,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282494,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH2 DRT S4 L002 I1 001.fastq.gz   read2PairFiles=DMH2 DRT S4 L002 R1 001.fastq.gz   read3PairFiles=DMH2 DRT S4 L002 R2 001.fastq.gz,DMH2_DRT_S4_L002_I1_001.fastq.gz DMH2_DRT_S4_L002_R1_001.fastq.gz DMH2_DRT_S4_L002_R2_001.fastq.gz,fastq fastq fastq,6646362882.0,52333566.0,GSM5282494 r2,0:8 1:28 2:91,A:1846304900;C:1444524063;G:1542630967;T:1810887938;N:2015014,8,28,91,,1846304900,1444524063,1542630967,1810887938,2015014,SRX10779727,SRS8866160,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93778,,0.14911,,0.80014,,0.53536,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64305,SRR14428559,SRX10779727,SRS8866160,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 2,GSM5282494,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 2,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282494,GSM5282494: scRNA seq of  DMH1 treatment embryo replicate 2; Danio rerio; RNA Seq,GSM5282494,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282494,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH2 DRT S4 L003 I1 001.fastq.gz   read2PairFiles=DMH2 DRT S4 L003 R1 001.fastq.gz   read3PairFiles=DMH2 DRT S4 L003 R2 001.fastq.gz,DMH2_DRT_S4_L003_I1_001.fastq.gz DMH2_DRT_S4_L003_R1_001.fastq.gz DMH2_DRT_S4_L003_R2_001.fastq.gz,fastq fastq fastq,6270391447.0,49373161.0,GSM5282494 r3,0:8 1:28 2:91,A:1742421104;C:1361864013;G:1454871057;T:1709147257;N:2088016,8,28,91,,1742421104,1361864013,1454871057,1709147257,2088016,SRX10779727,SRS8866160,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93712,,0.14875,,0.79941,,0.53579,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64306,SRR14428560,SRX10779727,SRS8866160,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 2,GSM5282494,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 2,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282494,GSM5282494: scRNA seq of  DMH1 treatment embryo replicate 2; Danio rerio; RNA Seq,GSM5282494,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282494,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH2 DRT S4 L004 I1 001.fastq.gz   read2PairFiles=DMH2 DRT S4 L004 R1 001.fastq.gz   read3PairFiles=DMH2 DRT S4 L004 R2 001.fastq.gz,DMH2_DRT_S4_L004_I1_001.fastq.gz DMH2_DRT_S4_L004_R1_001.fastq.gz DMH2_DRT_S4_L004_R2_001.fastq.gz,fastq fastq fastq,5907875535.0,46518705.0,GSM5282494 r4,0:8 1:28 2:91,A:1640954912;C:1282401213;G:1370906184;T:1611398475;N:2214751,8,28,91,,1640954912,1282401213,1370906184,1611398475,2214751,SRX10779727,SRS8866160,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93572,,0.15069,,0.79955,,0.5303,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64307,SRR14428561,SRX10779727,SRS8866160,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 2,GSM5282494,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 2,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282494,GSM5282494: scRNA seq of  DMH1 treatment embryo replicate 2; Danio rerio; RNA Seq,GSM5282494,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282494,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH2 DRT S4 L005 I1 001.fastq.gz   read2PairFiles=DMH2 DRT S4 L005 R1 001.fastq.gz   read3PairFiles=DMH2 DRT S4 L005 R2 001.fastq.gz,DMH2_DRT_S4_L005_I1_001.fastq.gz DMH2_DRT_S4_L005_R1_001.fastq.gz DMH2_DRT_S4_L005_R2_001.fastq.gz,fastq fastq fastq,6282717178.0,49470214.0,GSM5282494 r5,0:8 1:28 2:91,A:1743975533;C:1365224270;G:1459015324;T:1711737289;N:2764762,8,28,91,,1743975533,1365224270,1459015324,1711737289,2764762,SRX10779727,SRS8866160,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93674,,0.14955,,0.79967,,0.53737,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64308,SRR14428562,SRX10779727,SRS8866160,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 2,GSM5282494,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 2,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282494,GSM5282494: scRNA seq of  DMH1 treatment embryo replicate 2; Danio rerio; RNA Seq,GSM5282494,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282494,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH2 DRT S4 L006 I1 001.fastq.gz   read2PairFiles=DMH2 DRT S4 L006 R1 001.fastq.gz   read3PairFiles=DMH2 DRT S4 L006 R2 001.fastq.gz,DMH2_DRT_S4_L006_I1_001.fastq.gz DMH2_DRT_S4_L006_R1_001.fastq.gz DMH2_DRT_S4_L006_R2_001.fastq.gz,fastq fastq fastq,5269518417.0,41492271.0,GSM5282494 r6,0:8 1:28 2:91,A:1464198453;C:1143221188;G:1221184805;T:1438563475;N:2350496,8,28,91,,1464198453,1143221188,1221184805,1438563475,2350496,SRX10779727,SRS8866160,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93742,,0.14919,,0.79845,,0.54799,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64309,SRR14428551,SRX10779726,SRS8866159,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 1,GSM5282493,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 1,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282493,GSM5282493: scRNA seq of  DMH1 treatment embryo replicate 1; Danio rerio; RNA Seq,GSM5282493,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282493,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH0 DRT S3 L001 I1 001.fastq.gz   read2PairFiles=DMH0 DRT S3 L001 R1 001.fastq.gz   read3PairFiles=DMH0 DRT S3 L001 R2 001.fastq.gz,DMH0_DRT_S3_L001_I1_001.fastq.gz DMH0_DRT_S3_L001_R1_001.fastq.gz DMH0_DRT_S3_L001_R2_001.fastq.gz,fastq fastq fastq,6300938503.0,49613689.0,GSM5282493 r1,0:8 1:28 2:91,A:1759925650;C:1368738360;G:1447709330;T:1722055328;N:2509835,8,28,91,,1759925650,1368738360,1447709330,1722055328,2509835,SRX10779726,SRS8866159,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.9327,,0.15731,,0.80342,,0.52216,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64310,SRR14428552,SRX10779726,SRS8866159,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 1,GSM5282493,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 1,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282493,GSM5282493: scRNA seq of  DMH1 treatment embryo replicate 1; Danio rerio; RNA Seq,GSM5282493,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282493,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH0 DRT S3 L002 I1 001.fastq.gz   read2PairFiles=DMH0 DRT S3 L002 R1 001.fastq.gz   read3PairFiles=DMH0 DRT S3 L002 R2 001.fastq.gz,DMH0_DRT_S3_L002_I1_001.fastq.gz DMH0_DRT_S3_L002_R1_001.fastq.gz DMH0_DRT_S3_L002_R2_001.fastq.gz,fastq fastq fastq,6688754085.0,52667355.0,GSM5282493 r2,0:8 1:28 2:91,A:1871898974;C:1453608653;G:1536025145;T:1825187880;N:2033433,8,28,91,,1871898974,1453608653,1536025145,1825187880,2033433,SRX10779726,SRS8866159,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93334,,0.1552,,0.80373,,0.50289,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64311,SRR14428553,SRX10779726,SRS8866159,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 1,GSM5282493,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 1,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282493,GSM5282493: scRNA seq of  DMH1 treatment embryo replicate 1; Danio rerio; RNA Seq,GSM5282493,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282493,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH0 DRT S3 L003 I1 001.fastq.gz   read2PairFiles=DMH0 DRT S3 L003 R1 001.fastq.gz   read3PairFiles=DMH0 DRT S3 L003 R2 001.fastq.gz,DMH0_DRT_S3_L003_I1_001.fastq.gz DMH0_DRT_S3_L003_R1_001.fastq.gz DMH0_DRT_S3_L003_R2_001.fastq.gz,fastq fastq fastq,6309453345.0,49680735.0,GSM5282493 r3,0:8 1:28 2:91,A:1763855982;C:1371096919;G:1449223687;T:1723174913;N:2101844,8,28,91,,1763855982,1371096919,1449223687,1723174913,2101844,SRX10779726,SRS8866159,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93296,,0.15857,,0.80129,,0.51279,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64312,SRR14428554,SRX10779726,SRS8866159,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 1,GSM5282493,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 1,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282493,GSM5282493: scRNA seq of  DMH1 treatment embryo replicate 1; Danio rerio; RNA Seq,GSM5282493,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282493,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH0 DRT S3 L004 I1 001.fastq.gz   read2PairFiles=DMH0 DRT S3 L004 R1 001.fastq.gz   read3PairFiles=DMH0 DRT S3 L004 R2 001.fastq.gz,DMH0_DRT_S3_L004_I1_001.fastq.gz DMH0_DRT_S3_L004_R1_001.fastq.gz DMH0_DRT_S3_L004_R2_001.fastq.gz,fastq fastq fastq,5945234490.0,46812870.0,GSM5282493 r4,0:8 1:28 2:91,A:1658145096;C:1291985068;G:1366762922;T:1626114511;N:2226893,8,28,91,,1658145096,1291985068,1366762922,1626114511,2226893,SRX10779726,SRS8866159,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93141,,0.15528,,0.80046,,0.51469,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64313,SRR14428555,SRX10779726,SRS8866159,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 1,GSM5282493,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 1,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282493,GSM5282493: scRNA seq of  DMH1 treatment embryo replicate 1; Danio rerio; RNA Seq,GSM5282493,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282493,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH0 DRT S3 L005 I1 001.fastq.gz   read2PairFiles=DMH0 DRT S3 L005 R1 001.fastq.gz   read3PairFiles=DMH0 DRT S3 L005 R2 001.fastq.gz,DMH0_DRT_S3_L005_I1_001.fastq.gz DMH0_DRT_S3_L005_R1_001.fastq.gz DMH0_DRT_S3_L005_R2_001.fastq.gz,fastq fastq fastq,6320557082.0,49768166.0,GSM5282493 r5,0:8 1:28 2:91,A:1763393223;C:1374562319;G:1453442879;T:1726374884;N:2783777,8,28,91,,1763393223,1374562319,1453442879,1726374884,2783777,SRX10779726,SRS8866159,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93108,,0.15583,,0.79797,,0.49781,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64314,SRR14428556,SRX10779726,SRS8866159,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of DMH1 treatment embryo replicate 1,GSM5282493,,tissue:tail|treatment:DMH1,scRNA seq of  DMH1 treatment embryo replicate 1,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:DMH1,GSM5282493,GSM5282493: scRNA seq of  DMH1 treatment embryo replicate 1; Danio rerio; RNA Seq,GSM5282493,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282493,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DMH0 DRT S3 L006 I1 001.fastq.gz   read2PairFiles=DMH0 DRT S3 L006 R1 001.fastq.gz   read3PairFiles=DMH0 DRT S3 L006 R2 001.fastq.gz,DMH0_DRT_S3_L006_I1_001.fastq.gz DMH0_DRT_S3_L006_R1_001.fastq.gz DMH0_DRT_S3_L006_R2_001.fastq.gz,fastq fastq fastq,5301340553.0,41742839.0,GSM5282493 r6,0:8 1:28 2:91,A:1476841423;C:1152107488;G:1217817934;T:1452213447;N:2360261,8,28,91,,1476841423,1152107488,1217817934,1452213447,2360261,SRX10779726,SRS8866159,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.93212,,0.15734,,0.79762,,0.5013,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64315,SRR14428547,SRX10779725,SRS8866158,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of Wild type embryo replicate 2,GSM5282492,,tissue:tail|treatment:WT,scRNA seq of Wild type embryo replicate 2,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:WT,GSM5282492,GSM5282492: scRNA seq of Wild type embryo replicate 2; Danio rerio; RNA Seq,GSM5282492,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282492,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DJ2 DRT S5 L005 I1 001.fastq.gz   read2PairFiles=DJ2 DRT S5 L005 R1 001.fastq.gz   read3PairFiles=DJ2 DRT S5 L005 R2 001.fastq.gz,DJ2_DRT_S5_L005_I1_001.fastq.gz DJ2_DRT_S5_L005_R1_001.fastq.gz DJ2_DRT_S5_L005_R2_001.fastq.gz,fastq fastq fastq,9467670930.0,74548590.0,GSM5282492 r1,0:8 1:28 2:91,A:2616039420;C:2044228336;G:2155133373;T:2648580130;N:3689671,8,28,91,,2616039420,2044228336,2155133373,2648580130,3689671,SRX10779725,SRS8866158,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92297,,0.1292,,0.79594,,0.47206,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64316,SRR14428548,SRX10779725,SRS8866158,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of Wild type embryo replicate 2,GSM5282492,,tissue:tail|treatment:WT,scRNA seq of Wild type embryo replicate 2,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:WT,GSM5282492,GSM5282492: scRNA seq of Wild type embryo replicate 2; Danio rerio; RNA Seq,GSM5282492,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282492,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DJ2 DRT S5 L006 I1 001.fastq.gz   read2PairFiles=DJ2 DRT S5 L006 R1 001.fastq.gz   read3PairFiles=DJ2 DRT S5 L006 R2 001.fastq.gz,DJ2_DRT_S5_L006_I1_001.fastq.gz DJ2_DRT_S5_L006_R1_001.fastq.gz DJ2_DRT_S5_L006_R2_001.fastq.gz,fastq fastq fastq,9606615153.0,75642639.0,GSM5282492 r2,0:8 1:28 2:91,A:2652932569;C:2076799397;G:2185712596;T:2687420468;N:3750123,8,28,91,,2652932569,2076799397,2185712596,2687420468,3750123,SRX10779725,SRS8866158,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92257,,0.12971,,0.79659,,0.48836,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64317,SRR14428549,SRX10779725,SRS8866158,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of Wild type embryo replicate 2,GSM5282492,,tissue:tail|treatment:WT,scRNA seq of Wild type embryo replicate 2,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:WT,GSM5282492,GSM5282492: scRNA seq of Wild type embryo replicate 2; Danio rerio; RNA Seq,GSM5282492,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282492,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DJ2 DRT S5 L007 I1 001.fastq.gz   read2PairFiles=DJ2 DRT S5 L007 R1 001.fastq.gz   read3PairFiles=DJ2 DRT S5 L007 R2 001.fastq.gz,DJ2_DRT_S5_L007_I1_001.fastq.gz DJ2_DRT_S5_L007_R1_001.fastq.gz DJ2_DRT_S5_L007_R2_001.fastq.gz,fastq fastq fastq,9361056081.0,73709103.0,GSM5282492 r3,0:8 1:28 2:91,A:2586073553;C:2021754649;G:2129759929;T:2619378296;N:4089654,8,28,91,,2586073553,2021754649,2129759929,2619378296,4089654,SRX10779725,SRS8866158,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.92292,,0.12805,,0.79711,,0.48448,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64318,SRR14428550,SRX10779725,SRS8866158,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of Wild type embryo replicate 2,GSM5282492,,tissue:tail|treatment:WT,scRNA seq of Wild type embryo replicate 2,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:WT,GSM5282492,GSM5282492: scRNA seq of Wild type embryo replicate 2; Danio rerio; RNA Seq,GSM5282492,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282492,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DJ2 DRT S5 L008 I1 001.fastq.gz   read2PairFiles=DJ2 DRT S5 L008 R1 001.fastq.gz   read3PairFiles=DJ2 DRT S5 L008 R2 001.fastq.gz,DJ2_DRT_S5_L008_I1_001.fastq.gz DJ2_DRT_S5_L008_R1_001.fastq.gz DJ2_DRT_S5_L008_R2_001.fastq.gz,fastq fastq fastq,9160620617.0,72130871.0,GSM5282492 r4,0:8 1:28 2:91,A:2531032919;C:1977019121;G:2085046454;T:2562829034;N:4693089,8,28,91,,2531032919,1977019121,2085046454,2562829034,4693089,SRX10779725,SRS8866158,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.91651,,0.12813,,0.79525,,0.48008,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64319,SRR14428543,SRX10779724,SRS8866157,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of Wild type embryo replicate 1,GSM5282491,,tissue:tail|treatment:WT,scRNA seq of Wild type embryo replicate 1,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:WT,GSM5282491,GSM5282491: scRNA seq of Wild type embryo replicate 1; Danio rerio; RNA Seq,GSM5282491,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282491,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DJ1 DRT S4 L005 I1 001.fastq.gz   read2PairFiles=DJ1 DRT S4 L005 R1 001.fastq.gz   read3PairFiles=DJ1 DRT S4 L005 R2 001.fastq.gz,DJ1_DRT_S4_L005_I1_001.fastq.gz DJ1_DRT_S4_L005_R1_001.fastq.gz DJ1_DRT_S4_L005_R2_001.fastq.gz,fastq fastq fastq,9659035419.0,76055397.0,GSM5282491 r1,0:8 1:28 2:91,A:2699725431;C:2071581042;G:2198625287;T:2685342644;N:3761015,8,28,91,,2699725431,2071581042,2198625287,2685342644,3761015,SRX10779724,SRS8866157,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.91607,,0.12753,,0.79681,,0.49967,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64320,SRR14428544,SRX10779724,SRS8866157,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of Wild type embryo replicate 1,GSM5282491,,tissue:tail|treatment:WT,scRNA seq of Wild type embryo replicate 1,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:WT,GSM5282491,GSM5282491: scRNA seq of Wild type embryo replicate 1; Danio rerio; RNA Seq,GSM5282491,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282491,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DJ1 DRT S4 L006 I1 001.fastq.gz   read2PairFiles=DJ1 DRT S4 L006 R1 001.fastq.gz   read3PairFiles=DJ1 DRT S4 L006 R2 001.fastq.gz,DJ1_DRT_S4_L006_I1_001.fastq.gz DJ1_DRT_S4_L006_R1_001.fastq.gz DJ1_DRT_S4_L006_R2_001.fastq.gz,fastq fastq fastq,9813486723.0,77271549.0,GSM5282491 r2,0:8 1:28 2:91,A:2741133797;C:2108031651;G:2232840506;T:2727650204;N:3830565,8,28,91,,2741133797,2108031651,2232840506,2727650204,3830565,SRX10779724,SRS8866157,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.91637,,0.12716,,0.8002,,0.49381,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64321,SRR14428545,SRX10779724,SRS8866157,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of Wild type embryo replicate 1,GSM5282491,,tissue:tail|treatment:WT,scRNA seq of Wild type embryo replicate 1,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:WT,GSM5282491,GSM5282491: scRNA seq of Wild type embryo replicate 1; Danio rerio; RNA Seq,GSM5282491,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282491,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DJ1 DRT S4 L007 I1 001.fastq.gz   read2PairFiles=DJ1 DRT S4 L007 R1 001.fastq.gz   read3PairFiles=DJ1 DRT S4 L007 R2 001.fastq.gz,DJ1_DRT_S4_L007_I1_001.fastq.gz DJ1_DRT_S4_L007_R1_001.fastq.gz DJ1_DRT_S4_L007_R2_001.fastq.gz,fastq fastq fastq,9552161363.0,75213869.0,GSM5282491 r3,0:8 1:28 2:91,A:2669841244;C:2049417390;G:2172764722;T:2655952220;N:4185787,8,28,91,,2669841244,2049417390,2172764722,2655952220,4185787,SRX10779724,SRS8866157,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.9169,,0.1274,,0.79975,,0.48564,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system
64322,SRR14428546,SRX10779724,SRS8866157,SRP318543,PRJNA727493,Single cell gene expression analysis of zebrafish body elongation,GSE173894,Transcriptome Analysis,scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt  Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration  specifically inhibition of FGF  BMP  or Wnt signaling. For each treatment  we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.,,pubmed:37267354,,scRNA seq of Wild type embryo replicate 1,GSM5282491,,tissue:tail|treatment:WT,scRNA seq of Wild type embryo replicate 1,We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics  version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.,tail,Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type  FGF  or BMP inhibition or twelve tails for Wnt inhibition were pooled together.,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,,treatment:WT,GSM5282491,GSM5282491: scRNA seq of Wild type embryo replicate 1; Danio rerio; RNA Seq,GSM5282491,,1,Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16 nt 10x Barcode  iii a 10 nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM  the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded  full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 read 2 primer sequence were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1  while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.,GEO Accession:GSM5282491,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP318543,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=DJ1 DRT S4 L008 I1 001.fastq.gz   read2PairFiles=DJ1 DRT S4 L008 R1 001.fastq.gz   read3PairFiles=DJ1 DRT S4 L008 R2 001.fastq.gz,DJ1_DRT_S4_L008_I1_001.fastq.gz DJ1_DRT_S4_L008_R1_001.fastq.gz DJ1_DRT_S4_L008_R2_001.fastq.gz,fastq fastq fastq,9341088506.0,73551878.0,GSM5282491 r4,0:8 1:28 2:91,A:2610958437;C:2002300297;G:2125775231;T:2597251940;N:4802601,8,28,91,,2610958437,2002300297,2125775231,2597251940,4802601,SRX10779724,SRS8866157,SRA1228423,GEO,"Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University",1,0.91008,,0.12627,,0.79973,,0.49782,,91,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-05-05,Segmentation,Embryo,Tail,Multi-system