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86 rows where devstage_curation = "Segmentation" and tissue_curation_coarse = "Multi-system"

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tissue_curation 3

technology 3

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Multi-system · 86 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_selection 1

devstage_curation_coarse 1

devstage_curation 1

  • Segmentation · 86 ✖
Link 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 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 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 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 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 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 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 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 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 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 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
34551 34551 SRR32104356 SRX27449954 SRS23876475 SRP559533 PRJNA1214751 Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq] GSE287815 Transcriptome Analysis During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.       17hpf Positive CNC 3 GSM8751787   source name:cardiac neural crest from midbrain hindbrain boundary to somite 6|tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +|geo loc name:missing|collection date:missing 17hpf Positive CNC 3 Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples cardiac neural crest from midbrain hindbrain boundary to somite 6   mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry + GSM8751787 GSM8751787: 17hpf Positive CNC 3; Danio rerio; RNA Seq GSM8751787 r1 GSM8751787 1 mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP559533     Sox10_pos_17hpf_CNC_3_22028_combined_filtered.fastq.gz fastq 5836253400.0 58362534.0 GSM8751787 r1 0:100 A:1666874971;C:1250406201;G:1263794016;T:1655113176;N:65036 100       1666874971 1250406201 1263794016 1655113176 65036 SRX27449954 SRS23876475 SRA2058978 Martik Lab, Molecular and Cell Biology, University of California Berkeley Martik Lab, Molecular and Cell Biology, University of California Berkeley                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2025-01-23 Segmentation Embryo Multi-tissue Multi-system
34552 34552 SRR32104357 SRX27449953 SRS23876474 SRP559533 PRJNA1214751 Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq] GSE287815 Transcriptome Analysis During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.       17hpf Positive CNC 2 GSM8751786   source name:cardiac neural crest from midbrain hindbrain boundary to somite 6|tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +|geo loc name:missing|collection date:missing 17hpf Positive CNC 2 Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples cardiac neural crest from midbrain hindbrain boundary to somite 6   mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry + GSM8751786 GSM8751786: 17hpf Positive CNC 2; Danio rerio; RNA Seq GSM8751786 r1 GSM8751786 1 mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP559533     Sox10_pos_17hpf_CNC_2_21338_combined_filtered.fastq.gz fastq 2444486550.0 48889731.0 GSM8751786 r1 0:50 A:706384494;C:515182895;G:525593789;T:697319091;N:6281 50       706384494 515182895 525593789 697319091 6281 SRX27449953 SRS23876474 SRA2058978 Martik Lab, Molecular and Cell Biology, University of California Berkeley Martik Lab, Molecular and Cell Biology, University of California Berkeley                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2025-01-23 Segmentation Embryo Multi-tissue Multi-system
34553 34553 SRR32104358 SRX27449952 SRS23876472 SRP559533 PRJNA1214751 Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq] GSE287815 Transcriptome Analysis During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.       17hpf Positive CNC 1 GSM8751785   source name:cardiac neural crest from midbrain hindbrain boundary to somite 6|tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +|geo loc name:missing|collection date:missing 17hpf Positive CNC 1 Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples cardiac neural crest from midbrain hindbrain boundary to somite 6   mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry + GSM8751785 GSM8751785: 17hpf Positive CNC 1; Danio rerio; RNA Seq GSM8751785 r1 GSM8751785 1 mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP559533     Sox10_pos_17hpf_CNC_1_21309_combined_filtered.fastq.gz fastq 3136080950.0 62721619.0 GSM8751785 r1 0:50 A:867446661;C:707750289;G:716376649;T:844460193;N:47158 50       867446661 707750289 716376649 844460193 47158 SRX27449952 SRS23876472 SRA2058978 Martik Lab, Molecular and Cell Biology, University of California Berkeley Martik Lab, Molecular and Cell Biology, University of California Berkeley                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2025-01-23 Segmentation Embryo Multi-tissue Multi-system
39930 39930 SRR2392485 SRX1240714 SRS1067365 SRP063659 PRJNA295533 Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face GSE72985 Transcriptome Analysis Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…   pubmed:27058748   WT 20hpf DP GSM1876253   source name:Pharyngeal arches|tissue:Pharyngeal arches|developmental stage:embryo|age:20 hpf|genotype:WT|treatment:N1 WT 20hpf DP Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample Pharyngeal arches   GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.   tissue:Pharyngeal arches|developmental stage:embryo|age:20 hpf|genotype:WT|treatment:N1 GSM1876253 GSM1876253: WT 20hpf DP; Danio rerio; RNA Seq GSM1876253   1 GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC. GEO Accession:GSM1876253 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP063659     GC-51_L000_R2_001.fastq.gz GC-51_L000_R1_001.fastq.gz fastq fastq 8748773288.0 57557719.0 GSM1876253 r1 0:76 1:76 A:2470411775;C:1715400097;G:1801773754;T:2758442284;N:2745378 76 76     2470411775 1715400097 1801773754 2758442284 2745378 SRX1240714 SRS1067365 SRA297650 GEO Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California 2 0.9023 0.87479 0.11683 0.11569 0.75592 0.77327 0.48431 0.49574 76 76 B B biological fallback assumption illumina nextseq full_length cdna_unspecified smarter bulk unknown unknown   United States 2015-09-14 Segmentation Embryo Pharyngeal Arch Multi-system
60451 60451 SRR12283718 SRX8787097 SRS7055744 SRP273008 PRJNA647599 Transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo GSE154885 Transcriptome Analysis cDNA extracted from FACS sorted GFP positive cells taken from trunk region of 14hpf zebrafish embryo with transgenic reporter TgBACnkx2.2a:memGFP TgBAColig2:GFP or TgBACdbx1b:GFP Overall design: transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo   pubmed:33004519   TgBACdbx1b:GFP positive cells 2 GSM4681846   tissue:FACS sorted dbx1b + neural progenitors|age:14hpf|genotype:WT TgBACdbx1b:GFP positive cells 2 Sequenced reads were filtered by fastqc 0.11.3 then mapped to GRCz10 whole genome using bowtie 1.1.1 with parameters q n 2 l 28 e 1000 I 0 X 1000 k 1 m 200 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include gene names gene length mapped count unmapped count Supplementary files format and content: excel spreadsheet with gene names and transcript count in each sample FACS sorted dbx1b + neural progenitors   14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols   age:14hpf|genotype:WT GSM4681846 GSM4681846: TgBACdbx1b:GFP positive cells 2; Danio rerio; RNA Seq GSM4681846   1 14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4681846 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP273008     LIB018768_TRA00046531_S8_L002_R1.fastq LIB018768_TRA00046531_S8_L002_R2.fastq fastq fastq 2333457800.0 23334578.0 GSM4681846 r1 0:50 1:50 A:665714687;C:482177371;G:502528257;T:682738013;N:299472 50 50     665714687 482177371 502528257 682738013 299472 SRX8787097 SRS7055744 SRA1102160 GEO Sean Megason, Systems Biology, Harvard Medical School 2 0.84752 0.83215 0.23085 0.22303 0.76635 0.76997 0.6427 0.65075 50 50 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2020-07-22 Segmentation Embryo Multi-tissue Multi-system
60452 60452 SRR12283717 SRX8787096 SRS7055743 SRP273008 PRJNA647599 Transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo GSE154885 Transcriptome Analysis cDNA extracted from FACS sorted GFP positive cells taken from trunk region of 14hpf zebrafish embryo with transgenic reporter TgBACnkx2.2a:memGFP TgBAColig2:GFP or TgBACdbx1b:GFP Overall design: transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo   pubmed:33004519   TgBACdbx1b:GFP positive cells 1 GSM4681845   tissue:FACS sorted dbx1b + neural progenitors|age:14hpf|genotype:WT TgBACdbx1b:GFP positive cells 1 Sequenced reads were filtered by fastqc 0.11.3 then mapped to GRCz10 whole genome using bowtie 1.1.1 with parameters q n 2 l 28 e 1000 I 0 X 1000 k 1 m 200 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include gene names gene length mapped count unmapped count Supplementary files format and content: excel spreadsheet with gene names and transcript count in each sample FACS sorted dbx1b + neural progenitors   14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols   age:14hpf|genotype:WT GSM4681845 GSM4681845: TgBACdbx1b:GFP positive cells 1; Danio rerio; RNA Seq GSM4681845   1 14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4681845 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP273008     LIB018768_TRA00046530_S7_L002_R1.fastq LIB018768_TRA00046530_S7_L002_R2.fastq fastq fastq 1766472900.0 17664729.0 GSM4681845 r1 0:50 1:50 A:494774427;C:378835123;G:387031562;T:505606249;N:225539 50 50     494774427 378835123 387031562 505606249 225539 SRX8787096 SRS7055743 SRA1102160 GEO Sean Megason, Systems Biology, Harvard Medical School 2 0.86013 0.84612 0.18313 0.17713 0.77015 0.77532 0.64231 0.56308 50 50 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2020-07-22 Segmentation Embryo Multi-tissue Multi-system
60453 60453 SRR12283716 SRX8787095 SRS7055742 SRP273008 PRJNA647599 Transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo GSE154885 Transcriptome Analysis cDNA extracted from FACS sorted GFP positive cells taken from trunk region of 14hpf zebrafish embryo with transgenic reporter TgBACnkx2.2a:memGFP TgBAColig2:GFP or TgBACdbx1b:GFP Overall design: transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo   pubmed:33004519   TgBAColig2:GFP positive cells 2 GSM4681844   tissue:FACS sorted olig2 + neural progenitors|age:14hpf|genotype:WT TgBAColig2:GFP positive cells 2 Sequenced reads were filtered by fastqc 0.11.3 then mapped to GRCz10 whole genome using bowtie 1.1.1 with parameters q n 2 l 28 e 1000 I 0 X 1000 k 1 m 200 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include gene names gene length mapped count unmapped count Supplementary files format and content: excel spreadsheet with gene names and transcript count in each sample FACS sorted olig2 + neural progenitors   14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols   age:14hpf|genotype:WT GSM4681844 GSM4681844: TgBAColig2:GFP positive cells 2; Danio rerio; RNA Seq GSM4681844   1 14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4681844 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP273008     LIB018768_TRA00046535_S12_L002_R1.fastq LIB018768_TRA00046535_S12_L002_R2.fastq fastq fastq 1883562500.0 18835625.0 GSM4681844 r1 0:50 1:50 A:538880974;C:389273777;G:399233943;T:555933855;N:239951 50 50     538880974 389273777 399233943 555933855 239951 SRX8787095 SRS7055742 SRA1102160 GEO Sean Megason, Systems Biology, Harvard Medical School 2 0.83434 0.81762 0.28607 0.27612 0.77804 0.78137 0.67234 0.67724 50 50 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2020-07-22 Segmentation Embryo Multi-tissue Multi-system
60454 60454 SRR12283715 SRX8787094 SRS7055741 SRP273008 PRJNA647599 Transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo GSE154885 Transcriptome Analysis cDNA extracted from FACS sorted GFP positive cells taken from trunk region of 14hpf zebrafish embryo with transgenic reporter TgBACnkx2.2a:memGFP TgBAColig2:GFP or TgBACdbx1b:GFP Overall design: transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo   pubmed:33004519   TgBAColig2:GFP positive cells 1 GSM4681843   tissue:FACS sorted olig2 + neural progenitors|age:14hpf|genotype:WT TgBAColig2:GFP positive cells 1 Sequenced reads were filtered by fastqc 0.11.3 then mapped to GRCz10 whole genome using bowtie 1.1.1 with parameters q n 2 l 28 e 1000 I 0 X 1000 k 1 m 200 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include gene names gene length mapped count unmapped count Supplementary files format and content: excel spreadsheet with gene names and transcript count in each sample FACS sorted olig2 + neural progenitors   14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols   age:14hpf|genotype:WT GSM4681843 GSM4681843: TgBAColig2:GFP positive cells 1; Danio rerio; RNA Seq GSM4681843   1 14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4681843 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP273008     LIB018768_TRA00046532_S9_L002_R1.fastq LIB018768_TRA00046532_S9_L002_R2.fastq fastq fastq 1679123300.0 16791233.0 GSM4681843 r1 0:50 1:50 A:483066027;C:337334552;G:356429892;T:502080995;N:211834 50 50     483066027 337334552 356429892 502080995 211834 SRX8787094 SRS7055741 SRA1102160 GEO Sean Megason, Systems Biology, Harvard Medical School 2 0.82763 0.8109 0.27206 0.26478 0.78526 0.78851 0.70765 0.7123 50 50 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2020-07-22 Segmentation Embryo Multi-tissue Multi-system
60455 60455 SRR12283714 SRX8787093 SRS7055740 SRP273008 PRJNA647599 Transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo GSE154885 Transcriptome Analysis cDNA extracted from FACS sorted GFP positive cells taken from trunk region of 14hpf zebrafish embryo with transgenic reporter TgBACnkx2.2a:memGFP TgBAColig2:GFP or TgBACdbx1b:GFP Overall design: transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo   pubmed:33004519   TgBACnkx2.2a:memGFP positive cells 2 GSM4681842   tissue:FACS sorted nkx2.2a + neural progenitors|age:14hpf|genotype:WT TgBACnkx2.2a:memGFP positive cells 2 Sequenced reads were filtered by fastqc 0.11.3 then mapped to GRCz10 whole genome using bowtie 1.1.1 with parameters q n 2 l 28 e 1000 I 0 X 1000 k 1 m 200 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include gene names gene length mapped count unmapped count Supplementary files format and content: excel spreadsheet with gene names and transcript count in each sample FACS sorted nkx2.2a + neural progenitors   14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols   age:14hpf|genotype:WT GSM4681842 GSM4681842: TgBACnkx2.2a:memGFP positive cells 2; Danio rerio; RNA Seq GSM4681842   1 14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4681842 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP273008     LIB018768_TRA00046534_S11_L002_R1.fastq LIB018768_TRA00046534_S11_L002_R2.fastq fastq fastq 1829250400.0 18292504.0 GSM4681842 r1 0:50 1:50 A:519439919;C:375677698;G:393002097;T:540898141;N:232545 50 50     519439919 375677698 393002097 540898141 232545 SRX8787093 SRS7055740 SRA1102160 GEO Sean Megason, Systems Biology, Harvard Medical School 2 0.83765 0.81845 0.28167 0.27377 0.79271 0.79563 0.73414 0.73464 50 50 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2020-07-22 Segmentation Embryo Multi-tissue Multi-system
60456 60456 SRR12283713 SRX8787092 SRS7055739 SRP273008 PRJNA647599 Transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo GSE154885 Transcriptome Analysis cDNA extracted from FACS sorted GFP positive cells taken from trunk region of 14hpf zebrafish embryo with transgenic reporter TgBACnkx2.2a:memGFP TgBAColig2:GFP or TgBACdbx1b:GFP Overall design: transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo   pubmed:33004519   TgBACnkx2.2a:memGFP positive cells 1 GSM4681841   tissue:FACS sorted nkx2.2a + neural progenitors|age:14hpf|genotype:WT TgBACnkx2.2a:memGFP positive cells 1 Sequenced reads were filtered by fastqc 0.11.3 then mapped to GRCz10 whole genome using bowtie 1.1.1 with parameters q n 2 l 28 e 1000 I 0 X 1000 k 1 m 200 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include gene names gene length mapped count unmapped count Supplementary files format and content: excel spreadsheet with gene names and transcript count in each sample FACS sorted nkx2.2a + neural progenitors   14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols   age:14hpf|genotype:WT GSM4681841 GSM4681841: TgBACnkx2.2a:memGFP positive cells 1; Danio rerio; RNA Seq GSM4681841   1 14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4681841 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP273008     LIB018768_TRA00046533_S10_L002_R1.fastq LIB018768_TRA00046533_S10_L002_R2.fastq fastq fastq 2075770200.0 20757702.0 GSM4681841 r1 0:50 1:50 A:595497281;C:427137535;G:443303257;T:609571756;N:260371 50 50     595497281 427137535 443303257 609571756 260371 SRX8787092 SRS7055739 SRA1102160 GEO Sean Megason, Systems Biology, Harvard Medical School 2 0.8636 0.84947 0.24936 0.2423 0.7568 0.76031 0.67066 0.6717 50 50 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2020-07-22 Segmentation Embryo Multi-tissue Multi-system
63226 63226 SRR13660516 SRX10052201 SRS8215327 SRP305389 PRJNA700672 Endothelial progenitor migration and differentiation is regulated by distinct transcriptional effectors of Cloche/Npas4l GSE166396 Transcriptome Analysis Embryonic cells including endothelial progenitors undergo extensive migration and differentiation events; however whether and how these processes are interrelated remains unclear. The transcription factor Npas4l is necessary for endothelial specification in zebrafish by inducing the expression of the transcription factor genes etsrp tal1 and lmo2. We generated a knock in reporter in the npas4l locus to visualize endothelial progenitors and their derivatives in wild type and mutant embryos. We find that in npas4l mutants npas4l reporter expressing cells do not migrate to the midline and instead contribute to skeletal muscle and pronephric tubules. Investigating the Npas4l transcriptional effectors we find that npas4l reporter expressing cells in tal1 mutants fail to migrate while those in etsrp mutants migrate but fail to differentiate. In lmo2 mutants npas4l reporter expressing cells migrate and differentiate but many express pronephric tubule markers. Altogether these data reveal the complex regulation of endothelial progenitor migration differentiation and fate restriction. Overall design: Comparison of npas4l reporter positive cells from heterozygous and homozygous npas4l mutant embryos using single cell RNAseq on sorted cells.       npas4l mut GSM5070576   tissue:npas4l reporter positive cells|cell type:sorted npas4l reporter positive cells|Stage:20 hpf npas4l mut Reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo followed by secondary analysis in Annotated Data Format. Preprocessed counts were further analysed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed only 16 cells in total that did not express between 1000 and 7000 genes or had an mitochondrial content less than 6%. Further we filtered genes if they were detected in less than 30 cells <0.3%. Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA retaining 50 principal components. Subsequent steps like low dimensional UMAP embedding and cell clustering via community detection were based on the initial PCA. Final data visualization was done by scVelo and cellxgene packages. Genome build: DanRer11 Supplementary files format and content: Mattonet adata obs.csv: basic anndata observations Sample n genes by counts log1p total counts pct counts is mito n genes detected leiden clustering Supplementary files format and content: Mattonet udata obs.csv: velocity anmdata observations initial size unspliced initial size spliced initial size n counts velocity self transition root cells end points velocity pseudotime npas4l reporter positive cells   Tails from 150 npas4l heterozygous npas4lbns423/+ and trans heterozygous npas4lbns423/bns297 mutant embryos were cut at the anterior end of the yolk extension at 20 hpf in DMEM/F10+5%FBS+0.01% tricaine on agarose coated plates. The cells were dissociated using the Pierce Cardiomyocyte dissociation kit according to manufacturer instructions and FACS sorted for GFP fluorescence using an AriaIII sorter and DAPI as indicator for dead cells. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer’s protocol to obtain 5000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol.   cell type:sorted npas4l reporter positive cells|Stage:20 hpf GSM5070576 GSM5070576: npas4l mut; Danio rerio; RNA Seq GSM5070576   1 Tails from 150 npas4l heterozygous npas4lbns423/+ and trans heterozygous npas4lbns423/bns297 mutant embryos were cut at the anterior end of the yolk extension at 20 hpf in DMEM/F10+5%FBS+0.01% tricaine on agarose coated plates. The cells were dissociated using the Pierce Cardiomyocyte dissociation kit according to manufacturer instructions and FACS sorted for GFP fluorescence using an AriaIII sorter and DAPI as indicator for dead cells. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer's protocol to obtain 5000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol. GEO Accession:GSM5070576 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP305389     Kenny_scRNA_Mut_BC.fastq.gz Kenny_scRNA_Mut_cDNA.fastq.gz fastq fastq 15859812024.0 188807286.0 GSM5070576 r1 0:28 1:56 A:4422689365;C:3447909764;G:3545664942;T:4438912669;N:4635284 28 56     4422689365 3447909764 3545664942 4438912669 4635284 SRX10052201 SRS8215327 SRA1193720 GEO MPI for heart and lung research 2 0.00208 0.92256 0.00079 0.14522 0.99602 0.81554 0.38888 0.49915 28 56 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2021-02-08 Segmentation Embryo Multi-tissue Multi-system
63227 63227 SRR13660515 SRX10052200 SRS8215328 SRP305389 PRJNA700672 Endothelial progenitor migration and differentiation is regulated by distinct transcriptional effectors of Cloche/Npas4l GSE166396 Transcriptome Analysis Embryonic cells including endothelial progenitors undergo extensive migration and differentiation events; however whether and how these processes are interrelated remains unclear. The transcription factor Npas4l is necessary for endothelial specification in zebrafish by inducing the expression of the transcription factor genes etsrp tal1 and lmo2. We generated a knock in reporter in the npas4l locus to visualize endothelial progenitors and their derivatives in wild type and mutant embryos. We find that in npas4l mutants npas4l reporter expressing cells do not migrate to the midline and instead contribute to skeletal muscle and pronephric tubules. Investigating the Npas4l transcriptional effectors we find that npas4l reporter expressing cells in tal1 mutants fail to migrate while those in etsrp mutants migrate but fail to differentiate. In lmo2 mutants npas4l reporter expressing cells migrate and differentiate but many express pronephric tubule markers. Altogether these data reveal the complex regulation of endothelial progenitor migration differentiation and fate restriction. Overall design: Comparison of npas4l reporter positive cells from heterozygous and homozygous npas4l mutant embryos using single cell RNAseq on sorted cells.       npas4l het GSM5070575   tissue:npas4l reporter positive cells|cell type:sorted npas4l reporter positive cells|Stage:20 hpf npas4l het Reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo followed by secondary analysis in Annotated Data Format. Preprocessed counts were further analysed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed only 16 cells in total that did not express between 1000 and 7000 genes or had an mitochondrial content less than 6%. Further we filtered genes if they were detected in less than 30 cells <0.3%. Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA retaining 50 principal components. Subsequent steps like low dimensional UMAP embedding and cell clustering via community detection were based on the initial PCA. Final data visualization was done by scVelo and cellxgene packages. Genome build: DanRer11 Supplementary files format and content: Mattonet adata obs.csv: basic anndata observations Sample n genes by counts log1p total counts pct counts is mito n genes detected leiden clustering Supplementary files format and content: Mattonet udata obs.csv: velocity anmdata observations initial size unspliced initial size spliced initial size n counts velocity self transition root cells end points velocity pseudotime npas4l reporter positive cells   Tails from 150 npas4l heterozygous npas4lbns423/+ and trans heterozygous npas4lbns423/bns297 mutant embryos were cut at the anterior end of the yolk extension at 20 hpf in DMEM/F10+5%FBS+0.01% tricaine on agarose coated plates. The cells were dissociated using the Pierce Cardiomyocyte dissociation kit according to manufacturer instructions and FACS sorted for GFP fluorescence using an AriaIII sorter and DAPI as indicator for dead cells. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer’s protocol to obtain 5000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol.   cell type:sorted npas4l reporter positive cells|Stage:20 hpf GSM5070575 GSM5070575: npas4l het; Danio rerio; RNA Seq GSM5070575   1 Tails from 150 npas4l heterozygous npas4lbns423/+ and trans heterozygous npas4lbns423/bns297 mutant embryos were cut at the anterior end of the yolk extension at 20 hpf in DMEM/F10+5%FBS+0.01% tricaine on agarose coated plates. The cells were dissociated using the Pierce Cardiomyocyte dissociation kit according to manufacturer instructions and FACS sorted for GFP fluorescence using an AriaIII sorter and DAPI as indicator for dead cells. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer's protocol to obtain 5000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol. GEO Accession:GSM5070575 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP305389     Kenny_scRNA_Het_BC.fastq.gz Kenny_scRNA_Het_cDNA.fastq.gz fastq fastq 21384880020.0 254581905.0 GSM5070575 r1 0:28 1:56 A:5828925615;C:4816199698;G:4885826464;T:5847660976;N:6267267 28 56     5828925615 4816199698 4885826464 5847660976 6267267 SRX10052200 SRS8215328 SRA1193720 GEO MPI for heart and lung research 2 0.00213 0.9288 0.00071 0.11864 0.99559 0.8312 0.43162 0.47914 28 56 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2021-02-08 Segmentation Embryo Multi-tissue Multi-system
63865 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 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 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 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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 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…   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 thr… 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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;