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74 rows where devstage_curation = "Segmentation" and tissue_curation = "Tail"

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  • Tail · 74 ✖

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devstage_curation_coarse 1

devstage_curation 1

  • Segmentation · 74 ✖
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
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");;