run_metadata
90 rows where experiment.library_strategy = "RNA-Seq" and technology = "fluidigm"
This data as json, CSV (advanced)
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 40168 | 40168 | SRR2968466 | SRX1457885 | SRS1185406 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP40 | GSM1959709 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP40 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959709 | GSM1959709: Sample KP40; Danio rerio; RNA Seq | GSM1959709 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959709 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP40_CAGAGAGG-ACTGCATA_R1.fastq.gz KP40_CAGAGAGG-ACTGCATA_R2.fastq.gz | fastq fastq | 1057620252.0 | 10368826.0 | GSM1959709 r1 | 0:51 1:51 | A:283533359;C:244321250;G:245847121;T:283599722;N:318800 | 51 | 51 | 283533359 | 244321250 | 245847121 | 283599722 | 318800 | SRX1457885 | SRS1185406 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.76357 | 0.76735 | 0.13867 | 0.14039 | 0.82655 | 0.82964 | 0.48721 | 0.44534 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40169 | 40169 | SRR2968465 | SRX1457884 | SRS1185407 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP39 | GSM1959708 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP39 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959708 | GSM1959708: Sample KP39; Danio rerio; RNA Seq | GSM1959708 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959708 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP39_CAGAGAGG-GTAAGGAG_R1.fastq.gz KP39_CAGAGAGG-GTAAGGAG_R2.fastq.gz | fastq fastq | 836720892.0 | 8203146.0 | GSM1959708 r1 | 0:51 1:51 | A:233855273;C:181887230;G:183940925;T:236839998;N:197466 | 51 | 51 | 233855273 | 181887230 | 183940925 | 236839998 | 197466 | SRX1457884 | SRS1185407 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.74388 | 0.75136 | 0.34441 | 0.34905 | 0.97173 | 0.97246 | 0.57093 | 0.57077 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40170 | 40170 | SRR2968464 | SRX1457883 | SRS1185408 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP38 | GSM1959707 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP38 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959707 | GSM1959707: Sample KP38; Danio rerio; RNA Seq | GSM1959707 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959707 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP38_CAGAGAGG-AGAGTAGA_R1.fastq.gz KP38_CAGAGAGG-AGAGTAGA_R2.fastq.gz | fastq fastq | 835878168.0 | 8194884.0 | GSM1959707 r1 | 0:51 1:51 | A:230311138;C:186569541;G:187836943;T:230971761;N:188785 | 51 | 51 | 230311138 | 186569541 | 187836943 | 230971761 | 188785 | SRX1457883 | SRS1185408 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.80225 | 0.80655 | 0.23659 | 0.24176 | 0.95343 | 0.95503 | 0.44336 | 0.43957 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40171 | 40171 | SRR2968463 | SRX1457882 | SRS1185409 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP37 | GSM1959706 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP37 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959706 | GSM1959706: Sample KP37; Danio rerio; RNA Seq | GSM1959706 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959706 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP37_CAGAGAGG-TATCCTCT_R1.fastq.gz KP37_CAGAGAGG-TATCCTCT_R2.fastq.gz | fastq fastq | 802409316.0 | 7866758.0 | GSM1959706 r1 | 0:51 1:51 | A:219583488;C:179155768;G:180744232;T:222683589;N:242239 | 51 | 51 | 219583488 | 179155768 | 180744232 | 222683589 | 242239 | SRX1457882 | SRS1185409 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.70494 | 0.71211 | 0.22141 | 0.22563 | 0.96895 | 0.96928 | 0.44073 | 0.4369 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40172 | 40172 | SRR2968462 | SRX1457881 | SRS1185410 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP36 | GSM1959705 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP36 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959705 | GSM1959705: Sample KP36; Danio rerio; RNA Seq | GSM1959705 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959705 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP36_CAGAGAGG-CTCTCTAT_R1.fastq.gz KP36_CAGAGAGG-CTCTCTAT_R2.fastq.gz | fastq fastq | 814437360.0 | 7984680.0 | GSM1959705 r1 | 0:51 1:51 | A:224134814;C:180827198;G:181990353;T:227245779;N:239216 | 51 | 51 | 224134814 | 180827198 | 181990353 | 227245779 | 239216 | SRX1457881 | SRS1185410 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.58241 | 0.59172 | 0.29636 | 0.30375 | 0.97991 | 0.98096 | 0.5342 | 0.54149 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40173 | 40173 | SRR2968461 | SRX1457880 | SRS1185411 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP35 | GSM1959704 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP35 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959704 | GSM1959704: Sample KP35; Danio rerio; RNA Seq | GSM1959704 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959704 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP35_CTCTCTAC-ACTGCATA_R1.fastq.gz KP35_CTCTCTAC-ACTGCATA_R2.fastq.gz | fastq fastq | 879876990.0 | 8626245.0 | GSM1959704 r1 | 0:51 1:51 | A:242880860;C:194901817;G:196696322;T:245139130;N:258861 | 51 | 51 | 242880860 | 194901817 | 196696322 | 245139130 | 258861 | SRX1457880 | SRS1185411 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.73158 | 0.737 | 0.31522 | 0.32009 | 0.9671 | 0.96855 | 0.49896 | 0.50832 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40174 | 40174 | SRR2968460 | SRX1457879 | SRS1185412 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP34 | GSM1959703 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP34 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959703 | GSM1959703: Sample KP34; Danio rerio; RNA Seq | GSM1959703 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959703 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP34_CTCTCTAC-GTAAGGAG_R1.fastq.gz KP34_CTCTCTAC-GTAAGGAG_R2.fastq.gz | fastq fastq | 530302590.0 | 5199045.0 | GSM1959703 r1 | 0:51 1:51 | A:125449980;C:137910409;G:138880104;T:127935495;N:126602 | 51 | 51 | 125449980 | 137910409 | 138880104 | 127935495 | 126602 | SRX1457879 | SRS1185412 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.09313 | 0.09794 | 0.01332 | 0.01452 | 0.99243 | 0.9932 | 0.93637 | 0.93172 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40175 | 40175 | SRR2968459 | SRX1457878 | SRS1185413 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP33 | GSM1959702 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP33 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959702 | GSM1959702: Sample KP33; Danio rerio; RNA Seq | GSM1959702 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959702 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP33_CTCTCTAC-AGAGTAGA_R1.fastq.gz KP33_CTCTCTAC-AGAGTAGA_R2.fastq.gz | fastq fastq | 702121590.0 | 6883545.0 | GSM1959702 r1 | 0:51 1:51 | A:177259877;C:172663803;G:174696764;T:177343178;N:157968 | 51 | 51 | 177259877 | 172663803 | 174696764 | 177343178 | 157968 | SRX1457878 | SRS1185413 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.51385 | 0.52475 | 0.02387 | 0.02469 | 0.98662 | 0.988 | 0.33323 | 0.26048 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40176 | 40176 | SRR2968458 | SRX1457877 | SRS1185414 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP32 | GSM1959701 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP32 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959701 | GSM1959701: Sample KP32; Danio rerio; RNA Seq | GSM1959701 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959701 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP32_CTCTCTAC-TATCCTCT_R1.fastq.gz KP32_CTCTCTAC-TATCCTCT_R2.fastq.gz | fastq fastq | 841118214.0 | 8246257.0 | GSM1959701 r1 | 0:51 1:51 | A:226923227;C:192290067;G:193443501;T:228207490;N:253929 | 51 | 51 | 226923227 | 192290067 | 193443501 | 228207490 | 253929 | SRX1457877 | SRS1185414 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.68864 | 0.69538 | 0.16992 | 0.173 | 0.97378 | 0.97445 | 0.43009 | 0.42506 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40177 | 40177 | SRR2968457 | SRX1457876 | SRS1185415 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP31 | GSM1959700 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP31 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959700 | GSM1959700: Sample KP31; Danio rerio; RNA Seq | GSM1959700 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959700 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP31_CTCTCTAC-CTCTCTAT_R1.fastq.gz KP31_CTCTCTAC-CTCTCTAT_R2.fastq.gz | fastq fastq | 897671706.0 | 8800703.0 | GSM1959700 r1 | 0:51 1:51 | A:246982191;C:200919612;G:202035872;T:247462202;N:271829 | 51 | 51 | 246982191 | 200919612 | 202035872 | 247462202 | 271829 | SRX1457876 | SRS1185415 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.7947 | 0.7971 | 0.23998 | 0.24233 | 0.9625 | 0.96307 | 0.43428 | 0.44592 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40178 | 40178 | SRR2968456 | SRX1457875 | SRS1185416 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP30 | GSM1959699 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP30 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959699 | GSM1959699: Sample KP30; Danio rerio; RNA Seq | GSM1959699 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959699 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP30_TAGGCATG-ACTGCATA_R1.fastq.gz KP30_TAGGCATG-ACTGCATA_R2.fastq.gz | fastq fastq | 840697464.0 | 8242132.0 | GSM1959699 r1 | 0:51 1:51 | A:229560852;C:189263205;G:190573999;T:231061385;N:238023 | 51 | 51 | 229560852 | 189263205 | 190573999 | 231061385 | 238023 | SRX1457875 | SRS1185416 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.7282 | 0.73495 | 0.19781 | 0.20144 | 0.96747 | 0.96846 | 0.4129 | 0.40756 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40179 | 40179 | SRR2968455 | SRX1457874 | SRS1185417 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP29 | GSM1959698 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP29 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959698 | GSM1959698: Sample KP29; Danio rerio; RNA Seq | GSM1959698 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959698 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP29_TAGGCATG-GTAAGGAG_R1.fastq.gz KP29_TAGGCATG-GTAAGGAG_R2.fastq.gz | fastq fastq | 731773602.0 | 7174251.0 | GSM1959698 r1 | 0:51 1:51 | A:206943127;C:156494362;G:158179677;T:209990471;N:165965 | 51 | 51 | 206943127 | 156494362 | 158179677 | 209990471 | 165965 | SRX1457874 | SRS1185417 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.65896 | 0.66545 | 0.44181 | 0.4484 | 0.97344 | 0.97374 | 0.39976 | 0.40584 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40180 | 40180 | SRR2968454 | SRX1457873 | SRS1185418 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP28 | GSM1959697 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP28 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959697 | GSM1959697: Sample KP28; Danio rerio; RNA Seq | GSM1959697 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959697 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP28_TAGGCATG-AGAGTAGA_R1.fastq.gz KP28_TAGGCATG-AGAGTAGA_R2.fastq.gz | fastq fastq | 610756314.0 | 5987807.0 | GSM1959697 r1 | 0:51 1:51 | A:168561813;C:135881390;G:137142260;T:169047160;N:123691 | 51 | 51 | 168561813 | 135881390 | 137142260 | 169047160 | 123691 | SRX1457873 | SRS1185418 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.82068 | 0.82379 | 0.2075 | 0.21165 | 0.95619 | 0.95789 | 0.43858 | 0.42372 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40181 | 40181 | SRR2968453 | SRX1457872 | SRS1185419 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP27 | GSM1959696 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP27 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959696 | GSM1959696: Sample KP27; Danio rerio; RNA Seq | GSM1959696 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959696 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP27_TAGGCATG-TATCCTCT_R1.fastq.gz KP27_TAGGCATG-TATCCTCT_R2.fastq.gz | fastq fastq | 781484424.0 | 7661612.0 | GSM1959696 r1 | 0:51 1:51 | A:212034731;C:176627403;G:178333528;T:214264629;N:224133 | 51 | 51 | 212034731 | 176627403 | 178333528 | 214264629 | 224133 | SRX1457872 | SRS1185419 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.61712 | 0.62713 | 0.23077 | 0.23648 | 0.9792 | 0.97944 | 0.39126 | 0.38932 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40182 | 40182 | SRR2968452 | SRX1457871 | SRS1185420 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP26 | GSM1959695 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP26 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959695 | GSM1959695: Sample KP26; Danio rerio; RNA Seq | GSM1959695 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959695 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP26_TAGGCATG-CTCTCTAT_R1.fastq.gz KP26_TAGGCATG-CTCTCTAT_R2.fastq.gz | fastq fastq | 780739926.0 | 7654313.0 | GSM1959695 r1 | 0:51 1:51 | A:218146933;C:170676228;G:171957248;T:219735082;N:224435 | 51 | 51 | 218146933 | 170676228 | 171957248 | 219735082 | 224435 | SRX1457871 | SRS1185420 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.78797 | 0.79538 | 0.35334 | 0.36142 | 0.96274 | 0.96349 | 0.47377 | 0.4735 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40183 | 40183 | SRR2968451 | SRX1457870 | SRS1185421 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP25 | GSM1959694 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP25 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959694 | GSM1959694: Sample KP25; Danio rerio; RNA Seq | GSM1959694 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959694 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP25_GGACTCCT-ACTGCATA_R1.fastq.gz KP25_GGACTCCT-ACTGCATA_R2.fastq.gz | fastq fastq | 859091634.0 | 8422467.0 | GSM1959694 r1 | 0:51 1:51 | A:236569798;C:191447789;G:192382830;T:238434022;N:257195 | 51 | 51 | 236569798 | 191447789 | 192382830 | 238434022 | 257195 | SRX1457870 | SRS1185421 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.759 | 0.76468 | 0.27302 | 0.27761 | 0.95554 | 0.95649 | 0.46406 | 0.47077 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40184 | 40184 | SRR2968450 | SRX1457869 | SRS1185422 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP24 | GSM1959693 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP24 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959693 | GSM1959693: Sample KP24; Danio rerio; RNA Seq | GSM1959693 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959693 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP24_GGACTCCT-GTAAGGAG_R1.fastq.gz KP24_GGACTCCT-GTAAGGAG_R2.fastq.gz | fastq fastq | 459382704.0 | 4503752.0 | GSM1959693 r1 | 0:51 1:51 | A:114887340;C:111878133;G:113634471;T:118873760;N:109000 | 51 | 51 | 114887340 | 111878133 | 113634471 | 118873760 | 109000 | SRX1457869 | SRS1185422 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.29195 | 0.30626 | 0.06586 | 0.07052 | 0.98397 | 0.98384 | 0.7621 | 0.75529 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40185 | 40185 | SRR2968449 | SRX1457868 | SRS1185423 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP23 | GSM1959692 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP23 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959692 | GSM1959692: Sample KP23; Danio rerio; RNA Seq | GSM1959692 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959692 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP23_GGACTCCT-AGAGTAGA_R1.fastq.gz KP23_GGACTCCT-AGAGTAGA_R2.fastq.gz | fastq fastq | 659521494.0 | 6465897.0 | GSM1959692 r1 | 0:51 1:51 | A:178790202;C:149883938;G:150983815;T:179718576;N:144963 | 51 | 51 | 178790202 | 149883938 | 150983815 | 179718576 | 144963 | SRX1457868 | SRS1185423 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.76779 | 0.77368 | 0.18286 | 0.18729 | 0.96948 | 0.96988 | 0.46781 | 0.47575 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40186 | 40186 | SRR2968448 | SRX1457867 | SRS1185424 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP22 | GSM1959691 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP22 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959691 | GSM1959691: Sample KP22; Danio rerio; RNA Seq | GSM1959691 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959691 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP22_GGACTCCT-TATCCTCT_R1.fastq.gz KP22_GGACTCCT-TATCCTCT_R2.fastq.gz | fastq fastq | 665437800.0 | 6523900.0 | GSM1959691 r1 | 0:51 1:51 | A:186143553;C:145046910;G:145792876;T:188254173;N:200288 | 51 | 51 | 186143553 | 145046910 | 145792876 | 188254173 | 200288 | SRX1457867 | SRS1185424 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.78988 | 0.7988 | 0.23272 | 0.23796 | 0.9613 | 0.9623 | 0.40863 | 0.41821 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40187 | 40187 | SRR2968447 | SRX1457866 | SRS1185425 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP21 | GSM1959690 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP21 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959690 | GSM1959690: Sample KP21; Danio rerio; RNA Seq | GSM1959690 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959690 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP21_GGACTCCT-CTCTCTAT_R1.fastq.gz KP21_GGACTCCT-CTCTCTAT_R2.fastq.gz | fastq fastq | 765085884.0 | 7500842.0 | GSM1959690 r1 | 0:51 1:51 | A:209306735;C:171106728;G:172589951;T:211844805;N:237665 | 51 | 51 | 209306735 | 171106728 | 172589951 | 211844805 | 237665 | SRX1457866 | SRS1185425 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.72371 | 0.73294 | 0.27277 | 0.27804 | 0.97143 | 0.97256 | 0.55072 | 0.54783 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40188 | 40188 | SRR2968446 | SRX1457865 | SRS1185426 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP20 | GSM1959689 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP20 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959689 | GSM1959689: Sample KP20; Danio rerio; RNA Seq | GSM1959689 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959689 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP20_TCCTGAGC-ACTGCATA_R1.fastq.gz KP20_TCCTGAGC-ACTGCATA_R2.fastq.gz | fastq fastq | 543216198.0 | 5325649.0 | GSM1959689 r1 | 0:51 1:51 | A:130111136;C:139338862;G:140806793;T:132795809;N:163598 | 51 | 51 | 130111136 | 139338862 | 140806793 | 132795809 | 163598 | SRX1457865 | SRS1185426 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.15752 | 0.16626 | 0.01611 | 0.01706 | 0.99062 | 0.99226 | 0.90887 | 0.90965 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40189 | 40189 | SRR2968445 | SRX1457864 | SRS1185427 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP19 | GSM1959688 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP19 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959688 | GSM1959688: Sample KP19; Danio rerio; RNA Seq | GSM1959688 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959688 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP19_TCCTGAGC-GTAAGGAG_R1.fastq.gz KP19_TCCTGAGC-GTAAGGAG_R2.fastq.gz | fastq fastq | 679334484.0 | 6660142.0 | GSM1959688 r1 | 0:51 1:51 | A:187051480;C:151121998;G:152297545;T:188715899;N:147562 | 51 | 51 | 187051480 | 151121998 | 152297545 | 188715899 | 147562 | SRX1457864 | SRS1185427 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.7866 | 0.79407 | 0.22875 | 0.23386 | 0.96575 | 0.96552 | 0.43227 | 0.45264 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40190 | 40190 | SRR2968444 | SRX1457863 | SRS1185428 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP18 | GSM1959687 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP18 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959687 | GSM1959687: Sample KP18; Danio rerio; RNA Seq | GSM1959687 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959687 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP18_TCCTGAGC-AGAGTAGA_R1.fastq.gz KP18_TCCTGAGC-AGAGTAGA_R2.fastq.gz | fastq fastq | 641049906.0 | 6284803.0 | GSM1959687 r1 | 0:51 1:51 | A:175031019;C:144143474;G:145394298;T:176339875;N:141240 | 51 | 51 | 175031019 | 144143474 | 145394298 | 176339875 | 141240 | SRX1457863 | SRS1185428 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.7934 | 0.79898 | 0.24196 | 0.2479 | 0.95893 | 0.9598 | 0.39391 | 0.39181 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40191 | 40191 | SRR2968443 | SRX1457862 | SRS1185429 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP17 | GSM1959686 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP17 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959686 | GSM1959686: Sample KP17; Danio rerio; RNA Seq | GSM1959686 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959686 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP17_TCCTGAGC-TATCCTCT_R1.fastq.gz KP17_TCCTGAGC-TATCCTCT_R2.fastq.gz | fastq fastq | 446775504.0 | 4380152.0 | GSM1959686 r1 | 0:51 1:51 | A:111578533;C:109198448;G:110776525;T:115086866;N:135132 | 51 | 51 | 111578533 | 109198448 | 110776525 | 115086866 | 135132 | SRX1457862 | SRS1185429 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.28419 | 0.29939 | 0.06797 | 0.07225 | 0.98289 | 0.98378 | 0.778 | 0.75243 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40192 | 40192 | SRR2968442 | SRX1457861 | SRS1185430 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP16 | GSM1959685 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP16 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959685 | GSM1959685: Sample KP16; Danio rerio; RNA Seq | GSM1959685 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959685 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP16_TCCTGAGC-CTCTCTAT_R1.fastq.gz KP16_TCCTGAGC-CTCTCTAT_R2.fastq.gz | fastq fastq | 692282466.0 | 6787083.0 | GSM1959685 r1 | 0:51 1:51 | A:189795491;C:154553440;G:155323657;T:192401712;N:208166 | 51 | 51 | 189795491 | 154553440 | 155323657 | 192401712 | 208166 | SRX1457861 | SRS1185430 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.79142 | 0.79731 | 0.16527 | 0.16819 | 0.95759 | 0.9572 | 0.4286 | 0.43086 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40193 | 40193 | SRR2968441 | SRX1457860 | SRS1185431 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP15 | GSM1959684 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP15 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959684 | GSM1959684: Sample KP15; Danio rerio; RNA Seq | GSM1959684 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959684 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP15_AGGCAGAA-ACTGCATA_R1.fastq.gz KP15_AGGCAGAA-ACTGCATA_R2.fastq.gz | fastq fastq | 809730570.0 | 7938535.0 | GSM1959684 r1 | 0:51 1:51 | A:222748248;C:181137297;G:181895010;T:223711434;N:238581 | 51 | 51 | 222748248 | 181137297 | 181895010 | 223711434 | 238581 | SRX1457860 | SRS1185431 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.82855 | 0.83316 | 0.19743 | 0.20117 | 0.933 | 0.93413 | 0.48016 | 0.48161 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40194 | 40194 | SRR2968440 | SRX1457859 | SRS1185432 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP14 | GSM1959683 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP14 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959683 | GSM1959683: Sample KP14; Danio rerio; RNA Seq | GSM1959683 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959683 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP14_AGGCAGAA-GTAAGGAG_R1.fastq.gz KP14_AGGCAGAA-GTAAGGAG_R2.fastq.gz | fastq fastq | 719230968.0 | 7051284.0 | GSM1959683 r1 | 0:51 1:51 | A:194927824;C:163566192;G:164765634;T:195815160;N:156158 | 51 | 51 | 194927824 | 163566192 | 164765634 | 195815160 | 156158 | SRX1457859 | SRS1185432 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.70333 | 0.71022 | 0.20537 | 0.20983 | 0.97437 | 0.97423 | 0.49029 | 0.49675 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40195 | 40195 | SRR2968439 | SRX1457858 | SRS1185433 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP13 | GSM1959682 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP13 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959682 | GSM1959682: Sample KP13; Danio rerio; RNA Seq | GSM1959682 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959682 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP13_AGGCAGAA-AGAGTAGA_R1.fastq.gz KP13_AGGCAGAA-AGAGTAGA_R2.fastq.gz | fastq fastq | 670420602.0 | 6572751.0 | GSM1959682 r1 | 0:51 1:51 | A:183200862;C:151496578;G:152546937;T:183041619;N:134606 | 51 | 51 | 183200862 | 151496578 | 152546937 | 183041619 | 134606 | SRX1457858 | SRS1185433 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.76244 | 0.76756 | 0.21376 | 0.21794 | 0.96544 | 0.96581 | 0.49113 | 0.50419 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40196 | 40196 | SRR2968438 | SRX1457857 | SRS1185434 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP12 | GSM1959681 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP12 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959681 | GSM1959681: Sample KP12; Danio rerio; RNA Seq | GSM1959681 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959681 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP12_AGGCAGAA-TATCCTCT_R1.fastq.gz KP12_AGGCAGAA-TATCCTCT_R2.fastq.gz | fastq fastq | 733517394.0 | 7191347.0 | GSM1959681 r1 | 0:51 1:51 | A:203973287;C:161740792;G:162503121;T:205085052;N:215142 | 51 | 51 | 203973287 | 161740792 | 162503121 | 205085052 | 215142 | SRX1457857 | SRS1185434 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.73987 | 0.74727 | 0.26293 | 0.26931 | 0.96692 | 0.96828 | 0.47118 | 0.48277 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40197 | 40197 | SRR2968437 | SRX1457856 | SRS1185435 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP11 | GSM1959680 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP11 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959680 | GSM1959680: Sample KP11; Danio rerio; RNA Seq | GSM1959680 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959680 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP11_AGGCAGAA-CTCTCTAT_R1.fastq.gz KP11_AGGCAGAA-CTCTCTAT_R2.fastq.gz | fastq fastq | 694641930.0 | 6810215.0 | GSM1959680 r1 | 0:51 1:51 | A:186479810;C:159537888;G:161650457;T:186768027;N:205748 | 51 | 51 | 186479810 | 159537888 | 161650457 | 186768027 | 205748 | SRX1457856 | SRS1185435 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.77343 | 0.7785 | 0.21899 | 0.22166 | 0.96591 | 0.96609 | 0.46452 | 0.49761 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40198 | 40198 | SRR2968436 | SRX1457855 | SRS1185436 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP10 | GSM1959679 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP10 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959679 | GSM1959679: Sample KP10; Danio rerio; RNA Seq | GSM1959679 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959679 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP10_CGTACTAG-ACTGCATA_R1.fastq.gz KP10_CGTACTAG-ACTGCATA_R2.fastq.gz | fastq fastq | 685215906.0 | 6717803.0 | GSM1959679 r1 | 0:51 1:51 | A:182783777;C:159470626;G:160436500;T:182320016;N:204987 | 51 | 51 | 182783777 | 159470626 | 160436500 | 182320016 | 204987 | SRX1457855 | SRS1185436 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.82772 | 0.83105 | 0.2043 | 0.20688 | 0.95373 | 0.95465 | 0.45406 | 0.44707 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40199 | 40199 | SRR2968435 | SRX1457854 | SRS1185437 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP9 | GSM1959678 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP9 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959678 | GSM1959678: Sample KP9; Danio rerio; RNA Seq | GSM1959678 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959678 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP9_CGTACTAG-GTAAGGAG_R1.fastq.gz KP9_CGTACTAG-GTAAGGAG_R2.fastq.gz | fastq fastq | 551932098.0 | 5411099.0 | GSM1959678 r1 | 0:51 1:51 | A:153342642;C:121303381;G:122377461;T:154778838;N:129776 | 51 | 51 | 153342642 | 121303381 | 122377461 | 154778838 | 129776 | SRX1457854 | SRS1185437 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.79709 | 0.80596 | 0.27077 | 0.27672 | 0.95 | 0.95142 | 0.47936 | 0.477 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40200 | 40200 | SRR2968434 | SRX1457853 | SRS1185398 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP8 | GSM1959677 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP8 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959677 | GSM1959677: Sample KP8; Danio rerio; RNA Seq | GSM1959677 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959677 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP8_CGTACTAG-AGAGTAGA_R1.fastq.gz KP8_CGTACTAG-AGAGTAGA_R2.fastq.gz | fastq fastq | 714534480.0 | 7005240.0 | GSM1959677 r1 | 0:51 1:51 | A:191434342;C:165417603;G:166779779;T:190738042;N:164714 | 51 | 51 | 191434342 | 165417603 | 166779779 | 190738042 | 164714 | SRX1457853 | SRS1185398 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.69731 | 0.70407 | 0.26985 | 0.27604 | 0.97417 | 0.97561 | 0.45016 | 0.44563 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40201 | 40201 | SRR2968433 | SRX1457852 | SRS1185399 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP7 | GSM1959676 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP7 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959676 | GSM1959676: Sample KP7; Danio rerio; RNA Seq | GSM1959676 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959676 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP7_CGTACTAG-TATCCTCT_R1.fastq.gz KP7_CGTACTAG-TATCCTCT_R2.fastq.gz | fastq fastq | 540102648.0 | 5295124.0 | GSM1959676 r1 | 0:51 1:51 | A:136000723;C:131024642;G:132847890;T:140063894;N:165499 | 51 | 51 | 136000723 | 131024642 | 132847890 | 140063894 | 165499 | SRX1457852 | SRS1185399 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.29483 | 0.30833 | 0.11533 | 0.12459 | 0.98307 | 0.9834 | 0.30473 | 0.30304 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40202 | 40202 | SRR2968432 | SRX1457851 | SRS1185402 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP6 | GSM1959675 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP6 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959675 | GSM1959675: Sample KP6; Danio rerio; RNA Seq | GSM1959675 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959675 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP6_CGTACTAG-CTCTCTAT_R1.fastq.gz KP6_CGTACTAG-CTCTCTAT_R2.fastq.gz | fastq fastq | 727623120.0 | 7133560.0 | GSM1959675 r1 | 0:51 1:51 | A:187458228;C:175169703;G:176202805;T:188567551;N:224833 | 51 | 51 | 187458228 | 175169703 | 176202805 | 188567551 | 224833 | SRX1457851 | SRS1185402 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.60168 | 0.60687 | 0.2039 | 0.20684 | 0.97589 | 0.97652 | 0.48458 | 0.48815 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40203 | 40203 | SRR2968431 | SRX1457850 | SRS1185400 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP5 | GSM1959674 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP5 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959674 | GSM1959674: Sample KP5; Danio rerio; RNA Seq | GSM1959674 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959674 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP5_TAAGGCGA-ACTGCATA_R1.fastq.gz KP5_TAAGGCGA-ACTGCATA_R2.fastq.gz | fastq fastq | 554516064.0 | 5436432.0 | GSM1959674 r1 | 0:51 1:51 | A:135355365;C:141324408;G:141559086;T:136117221;N:159984 | 51 | 51 | 135355365 | 141324408 | 141559086 | 136117221 | 159984 | SRX1457850 | SRS1185400 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.81675 | 0.8183 | 0.07186 | 0.07288 | 0.93695 | 0.93819 | 0.46802 | 0.47319 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40204 | 40204 | SRR2968430 | SRX1457849 | SRS1185401 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP4 | GSM1959673 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP4 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959673 | GSM1959673: Sample KP4; Danio rerio; RNA Seq | GSM1959673 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959673 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP4_TAAGGCGA-GTAAGGAG_R1.fastq.gz KP4_TAAGGCGA-GTAAGGAG_R2.fastq.gz | fastq fastq | 571891560.0 | 5606780.0 | GSM1959673 r1 | 0:51 1:51 | A:137779848;C:147767737;G:148621338;T:137588687;N:133950 | 51 | 51 | 137779848 | 147767737 | 148621338 | 137588687 | 133950 | SRX1457849 | SRS1185401 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.37677 | 0.384 | 0.09331 | 0.09568 | 0.9893 | 0.98936 | 0.52065 | 0.51305 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40205 | 40205 | SRR2968429 | SRX1457848 | SRS1185403 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP3 | GSM1959672 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP3 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959672 | GSM1959672: Sample KP3; Danio rerio; RNA Seq | GSM1959672 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959672 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP3_TAAGGCGA-AGAGTAGA_R1.fastq.gz KP3_TAAGGCGA-AGAGTAGA_R2.fastq.gz | fastq fastq | 452221590.0 | 4433545.0 | GSM1959672 r1 | 0:51 1:51 | A:114292214;C:111543381;G:112430113;T:113859372;N:96510 | 51 | 51 | 114292214 | 111543381 | 112430113 | 113859372 | 96510 | SRX1457848 | SRS1185403 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.76206 | 0.7667 | 0.1482 | 0.15259 | 0.96361 | 0.96477 | 0.42861 | 0.43397 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40206 | 40206 | SRR2968428 | SRX1457847 | SRS1185404 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP2 | GSM1959671 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP2 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959671 | GSM1959671: Sample KP2; Danio rerio; RNA Seq | GSM1959671 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959671 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP2_TAAGGCGA-TATCCTCT_R1.fastq.gz KP2_TAAGGCGA-TATCCTCT_R2.fastq.gz | fastq fastq | 497804574.0 | 4880437.0 | GSM1959671 r1 | 0:51 1:51 | A:127739086;C:120409728;G:121277399;T:128233124;N:145237 | 51 | 51 | 127739086 | 120409728 | 121277399 | 128233124 | 145237 | SRX1457847 | SRS1185404 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.72721 | 0.73133 | 0.19448 | 0.19789 | 0.96394 | 0.96441 | 0.42509 | 0.42064 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 40207 | 40207 | SRR2968427 | SRX1457846 | SRS1185405 | SRP066857 | PRJNA304633 | Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration | GSE75583 | Transcriptome Analysis | By contrast with mammals adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan epicardial and epicardial markers by alternative expression assays. Additionally we explored the function of the scaffolding protein and main component of caveolae caveolin 1 cav1 which was present in each epicardial subset. In BAC transgenic zebrafish cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy but displayed profound defects in injury induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers genetic tools and mechanisms of heart regeneration. Overall design: Deep sequencing of isolated single epicardial cells | pubmed:26657776 | Sample KP1 | GSM1959670 | source name:zebrafish epicardial cell|strain:EK|tissue:heart epicardium|age:6 month | Sample KP1 | Illumina CASAVA1.8 software used for basecalling. Sequenced reads were mapped to the zebrafish genome using Bowtie2. Transcript expressions were quantified by using RSEM 1.2.12 Genome build: Zv9 Supplementary files format and content: Tab delimited text files include expected count values for each sample. | zebrafish epicardial cell | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | strain:EK|tissue:heart epicardium|age:6 month | GSM1959670 | GSM1959670: Sample KP1; Danio rerio; RNA Seq | GSM1959670 | 1 | Ventricles were collected from adult tcf21:nucEGFP fish at 6 month of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH Roche and 1% sheep serum at 37°C while stirring gently with a Spinbar® magnetic stirring bar Bel Art Products. Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re suspended in DMEM plus 10% fetal bovine serum FBS medium with 1.5 μg/ml propidium iodide PI and sorted using a BD FACSVantage SE sorter for EGFP positive and PI negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol. Libraries were constructed on the C1 platform following the Fluidigm protocol. | GEO Accession:GSM1959670 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP066857 | KP1_TAAGGCGA-CTCTCTAT_R1.fastq.gz KP1_TAAGGCGA-CTCTCTAT_R2.fastq.gz | fastq fastq | 369456138.0 | 3622119.0 | GSM1959670 r1 | 0:51 1:51 | A:92118547;C:94231849;G:93842019;T:89151962;N:111761 | 51 | 51 | 92118547 | 94231849 | 93842019 | 89151962 | 111761 | SRX1457846 | SRS1185405 | SRA314385 | GEO | Kenneth Poss, Cell Biology, Duke University Medical Center | 2 | 0.32263 | 0.33307 | 0.00387 | 0.00402 | 0.99423 | 0.99521 | 0.98002 | 0.98282 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | fluidigm | United States | 2015-12-01 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 43663 | 43663 | SRR6025626 | SRX3176118 | SRS2505881 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 33775 | GSM2779358 | tissue:OMP positive bulk cells|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 33775 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive bulk cells | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779358 | GSM2779358: Sample 33775; Danio rerio; RNA Seq | GSM2779358 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779358 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s33775_R1.fastq.gz s33775_R2.fastq.gz | fastq fastq | 13661182750.0 | 54644731.0 | GSM2779358 r1 | 0:125 1:125 | A:3950172269;C:2838736020;G:2884461639;T:3801586863;N:186225959 | 125 | 125 | 3950172269 | 2838736020 | 2884461639 | 3801586863 | 186225959 | SRX3176118 | SRS2505881 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.3904 | 0.36122 | 0.09478 | 0.08957 | 0.84609 | 0.8744 | 0.59399 | 0.59594 | 125 | 125 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43664 | 43664 | SRR6025625 | SRX3176117 | SRS2505880 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 33774 | GSM2779357 | tissue:OMP positive bulk cells|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 33774 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive bulk cells | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779357 | GSM2779357: Sample 33774; Danio rerio; RNA Seq | GSM2779357 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779357 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s33774_R1.fastq.gz s33774_R2.fastq.gz | fastq fastq | 20456842250.0 | 81827369.0 | GSM2779357 r1 | 0:125 1:125 | A:5563992445;C:4574332893;G:4653958315;T:5384278584;N:280280013 | 125 | 125 | 5563992445 | 4574332893 | 4653958315 | 5384278584 | 280280013 | SRX3176117 | SRS2505880 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.31701 | 0.30885 | 0.06888 | 0.06856 | 0.87685 | 0.90228 | 0.64144 | 0.64023 | 125 | 125 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43665 | 43665 | SRR6025624 | SRX3176116 | SRS2505879 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 33773 | GSM2779356 | tissue:OMP positive bulk cells|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 33773 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive bulk cells | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779356 | GSM2779356: Sample 33773; Danio rerio; RNA Seq | GSM2779356 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779356 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s33773_R1.fastq.gz s33773_R2.fastq.gz | fastq fastq | 16320124000.0 | 65280496.0 | GSM2779356 r1 | 0:125 1:125 | A:4965742539;C:3472731005;G:3562901570;T:4084584782;N:234164104 | 125 | 125 | 4965742539 | 3472731005 | 3562901570 | 4084584782 | 234164104 | SRX3176116 | SRS2505879 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.33805 | 0.33895 | 0.08212 | 0.0862 | 0.92659 | 0.93628 | 0.67629 | 0.68777 | 125 | 125 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43666 | 43666 | SRR6025623 | SRX3176115 | SRS2505878 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23575 | GSM2779355 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23575 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779355 | GSM2779355: Sample 23575; Danio rerio; RNA Seq | GSM2779355 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779355 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23575_R1.fastq.gz s23575_R2.fastq.gz | fastq fastq | 12544724200.0 | 62723621.0 | GSM2779355 r1 | 0:100 1:100 | A:3618844414;C:2653220939;G:2611261038;T:3661178111;N:219698 | 100 | 100 | 3618844414 | 2653220939 | 2611261038 | 3661178111 | 219698 | SRX3176115 | SRS2505878 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.93157 | 0.92953 | 0.58399 | 0.58725 | 0.94836 | 0.9499 | 0.53141 | 0.54357 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43667 | 43667 | SRR6025622 | SRX3176114 | SRS2505877 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23574 | GSM2779354 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23574 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779354 | GSM2779354: Sample 23574; Danio rerio; RNA Seq | GSM2779354 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779354 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23574_R1.fastq.gz s23574_R2.fastq.gz | fastq fastq | 12628944800.0 | 63144724.0 | GSM2779354 r1 | 0:100 1:100 | A:3604039692;C:2698993964;G:2661293369;T:3664381683;N:236092 | 100 | 100 | 3604039692 | 2698993964 | 2661293369 | 3664381683 | 236092 | SRX3176114 | SRS2505877 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.92997 | 0.92999 | 0.56527 | 0.57132 | 0.95394 | 0.9554 | 0.49391 | 0.49038 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43668 | 43668 | SRR6025621 | SRX3176113 | SRS2505876 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23573 | GSM2779353 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23573 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779353 | GSM2779353: Sample 23573; Danio rerio; RNA Seq | GSM2779353 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779353 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23573_R1.fastq.gz s23573_R2.fastq.gz | fastq fastq | 11247992600.0 | 56239963.0 | GSM2779353 r1 | 0:100 1:100 | A:3267497015;C:2352817279;G:2318570280;T:3308902561;N:205465 | 100 | 100 | 3267497015 | 2352817279 | 2318570280 | 3308902561 | 205465 | SRX3176113 | SRS2505876 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.92371 | 0.92218 | 0.48304 | 0.49128 | 0.92957 | 0.93178 | 0.50806 | 0.51052 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43669 | 43669 | SRR6025620 | SRX3176112 | SRS2505875 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23572 | GSM2779352 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23572 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779352 | GSM2779352: Sample 23572; Danio rerio; RNA Seq | GSM2779352 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779352 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23572_R2.fastq.gz s23572_R1.fastq.gz | fastq fastq | 11219692000.0 | 56098460.0 | GSM2779352 r1 | 0:100 1:100 | A:3258674288;C:2339096536;G:2306091995;T:3315620058;N:209123 | 100 | 100 | 3258674288 | 2339096536 | 2306091995 | 3315620058 | 209123 | SRX3176112 | SRS2505875 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.91678 | 0.91488 | 0.61703 | 0.61868 | 0.94696 | 0.94966 | 0.50994 | 0.50873 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43670 | 43670 | SRR6025619 | SRX3176111 | SRS2505874 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23571 | GSM2779351 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23571 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779351 | GSM2779351: Sample 23571; Danio rerio; RNA Seq | GSM2779351 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779351 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23571_R1.fastq.gz s23571_R2.fastq.gz | fastq fastq | 13030579800.0 | 65152899.0 | GSM2779351 r1 | 0:100 1:100 | A:3722290207;C:2782988880;G:2744142531;T:3780916231;N:241951 | 100 | 100 | 3722290207 | 2782988880 | 2744142531 | 3780916231 | 241951 | SRX3176111 | SRS2505874 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.93208 | 0.93215 | 0.57822 | 0.58304 | 0.9572 | 0.9586 | 0.46862 | 0.48068 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43671 | 43671 | SRR6025618 | SRX3176110 | SRS2505873 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23570 | GSM2779350 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23570 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779350 | GSM2779350: Sample 23570; Danio rerio; RNA Seq | GSM2779350 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779350 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23570_R1.fastq.gz s23570_R2.fastq.gz | fastq fastq | 12121714600.0 | 60608573.0 | GSM2779350 r1 | 0:100 1:100 | A:3516410174;C:2524668105;G:2487242768;T:3593167208;N:226345 | 100 | 100 | 3516410174 | 2524668105 | 2487242768 | 3593167208 | 226345 | SRX3176110 | SRS2505873 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.91432 | 0.91459 | 0.68729 | 0.68793 | 0.95799 | 0.95994 | 0.6103 | 0.61469 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43672 | 43672 | SRR6025617 | SRX3176109 | SRS2505871 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23569 | GSM2779349 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23569 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779349 | GSM2779349: Sample 23569; Danio rerio; RNA Seq | GSM2779349 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779349 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23569_R1.fastq.gz s23569_R2.fastq.gz | fastq fastq | 13109319000.0 | 65546595.0 | GSM2779349 r1 | 0:100 1:100 | A:3781614875;C:2765399267;G:2726180320;T:3835879250;N:245288 | 100 | 100 | 3781614875 | 2765399267 | 2726180320 | 3835879250 | 245288 | SRX3176109 | SRS2505871 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.92553 | 0.92363 | 0.61103 | 0.61504 | 0.95047 | 0.95256 | 0.51779 | 0.51905 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43673 | 43673 | SRR6025616 | SRX3176108 | SRS2505872 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23568 | GSM2779348 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23568 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779348 | GSM2779348: Sample 23568; Danio rerio; RNA Seq | GSM2779348 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779348 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23568_R1.fastq.gz s23568_R2.fastq.gz | fastq fastq | 10809849800.0 | 54049249.0 | GSM2779348 r1 | 0:100 1:100 | A:3099873624;C:2301570943;G:2269311103;T:3138901271;N:192859 | 100 | 100 | 3099873624 | 2301570943 | 2269311103 | 3138901271 | 192859 | SRX3176108 | SRS2505872 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.93288 | 0.93209 | 0.54983 | 0.55527 | 0.95122 | 0.95286 | 0.54032 | 0.54826 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43674 | 43674 | SRR6025615 | SRX3176107 | SRS2505869 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23567 | GSM2779347 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23567 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779347 | GSM2779347: Sample 23567; Danio rerio; RNA Seq | GSM2779347 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779347 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23567_R1.fastq.gz s23567_R2.fastq.gz | fastq fastq | 10856209000.0 | 54281045.0 | GSM2779347 r1 | 0:100 1:100 | A:3101117015;C:2322206669;G:2293577151;T:3139111242;N:196923 | 100 | 100 | 3101117015 | 2322206669 | 2293577151 | 3139111242 | 196923 | SRX3176107 | SRS2505869 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.93023 | 0.92872 | 0.64291 | 0.6459 | 0.95793 | 0.95962 | 0.47236 | 0.51474 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43675 | 43675 | SRR6025614 | SRX3176106 | SRS2505870 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23566 | GSM2779346 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23566 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779346 | GSM2779346: Sample 23566; Danio rerio; RNA Seq | GSM2779346 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779346 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23566_R1.fastq.gz s23566_R2.fastq.gz | fastq fastq | 6524402000.0 | 32622010.0 | GSM2779346 r1 | 0:100 1:100 | A:1637781661;C:1626426425;G:1602187410;T:1657893406;N:113098 | 100 | 100 | 1637781661 | 1626426425 | 1602187410 | 1657893406 | 113098 | SRX3176106 | SRS2505870 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.95 | 0.94842 | 0.59579 | 0.59362 | 0.96453 | 0.96587 | 0.50083 | 0.50284 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43676 | 43676 | SRR6025613 | SRX3176105 | SRS2505868 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23565 | GSM2779345 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23565 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779345 | GSM2779345: Sample 23565; Danio rerio; RNA Seq | GSM2779345 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779345 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23565_R1.fastq.gz s23565_R2.fastq.gz | fastq fastq | 10387462200.0 | 51937311.0 | GSM2779345 r1 | 0:100 1:100 | A:2936142531;C:2240421768;G:2216761959;T:2993930182;N:205760 | 100 | 100 | 2936142531 | 2240421768 | 2216761959 | 2993930182 | 205760 | SRX3176105 | SRS2505868 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.91926 | 0.91982 | 0.66756 | 0.67009 | 0.95548 | 0.95737 | 0.53908 | 0.53171 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43677 | 43677 | SRR6025612 | SRX3176104 | SRS2505867 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23564 | GSM2779344 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23564 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779344 | GSM2779344: Sample 23564; Danio rerio; RNA Seq | GSM2779344 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779344 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23564_R1.fastq.gz s23564_R2.fastq.gz | fastq fastq | 14979643000.0 | 74898215.0 | GSM2779344 r1 | 0:100 1:100 | A:4264810263;C:3191982840;G:3161599788;T:4360950298;N:299811 | 100 | 100 | 4264810263 | 3191982840 | 3161599788 | 4360950298 | 299811 | SRX3176104 | SRS2505867 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.92995 | 0.93129 | 0.6183 | 0.62251 | 0.95917 | 0.95978 | 0.52498 | 0.52445 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43678 | 43678 | SRR6025611 | SRX3176103 | SRS2505866 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23563 | GSM2779343 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23563 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779343 | GSM2779343: Sample 23563; Danio rerio; RNA Seq | GSM2779343 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779343 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23563_R1.fastq.gz s23563_R2.fastq.gz | fastq fastq | 13158024200.0 | 65790121.0 | GSM2779343 r1 | 0:100 1:100 | A:3783048488;C:2775938640;G:2744155512;T:3854621841;N:259719 | 100 | 100 | 3783048488 | 2775938640 | 2744155512 | 3854621841 | 259719 | SRX3176103 | SRS2505866 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.92923 | 0.92877 | 0.56994 | 0.57248 | 0.9486 | 0.94925 | 0.53538 | 0.53999 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43679 | 43679 | SRR6025610 | SRX3176102 | SRS2505865 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23562 | GSM2779342 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23562 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779342 | GSM2779342: Sample 23562; Danio rerio; RNA Seq | GSM2779342 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779342 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23562_R1.fastq.gz s23562_R2.fastq.gz | fastq fastq | 12449365000.0 | 62246825.0 | GSM2779342 r1 | 0:100 1:100 | A:3533715755;C:2668392844;G:2636217587;T:3610782967;N:255847 | 100 | 100 | 3533715755 | 2668392844 | 2636217587 | 3610782967 | 255847 | SRX3176102 | SRS2505865 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.92882 | 0.92935 | 0.65434 | 0.65647 | 0.95889 | 0.95986 | 0.54424 | 0.54695 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43680 | 43680 | SRR6025609 | SRX3176101 | SRS2505864 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23561 | GSM2779341 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23561 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779341 | GSM2779341: Sample 23561; Danio rerio; RNA Seq | GSM2779341 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779341 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23561_R1.fastq.gz s23561_R2.fastq.gz | fastq fastq | 12799216000.0 | 63996080.0 | GSM2779341 r1 | 0:100 1:100 | A:3688996768;C:2684674464;G:2656843614;T:3768443466;N:257688 | 100 | 100 | 3688996768 | 2684674464 | 2656843614 | 3768443466 | 257688 | SRX3176101 | SRS2505864 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.91822 | 0.91905 | 0.60422 | 0.60709 | 0.95475 | 0.95574 | 0.56585 | 0.56751 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43681 | 43681 | SRR6025608 | SRX3176100 | SRS2505863 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23560 | GSM2779340 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23560 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779340 | GSM2779340: Sample 23560; Danio rerio; RNA Seq | GSM2779340 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779340 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23560_R1.fastq.gz s23560_R2.fastq.gz | fastq fastq | 13605105600.0 | 68025528.0 | GSM2779340 r1 | 0:100 1:100 | A:3874286570;C:2892667747;G:2852156877;T:3985718797;N:275609 | 100 | 100 | 3874286570 | 2892667747 | 2852156877 | 3985718797 | 275609 | SRX3176100 | SRS2505863 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.92952 | 0.92911 | 0.77695 | 0.77662 | 0.97254 | 0.97339 | 0.54961 | 0.55378 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43682 | 43682 | SRR6025607 | SRX3176099 | SRS2505862 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23559 | GSM2779339 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23559 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779339 | GSM2779339: Sample 23559; Danio rerio; RNA Seq | GSM2779339 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779339 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23559_R1.fastq.gz s23559_R2.fastq.gz | fastq fastq | 14038482800.0 | 70192414.0 | GSM2779339 r1 | 0:100 1:100 | A:3960290719;C:3025074892;G:2994349007;T:4058483161;N:285021 | 100 | 100 | 3960290719 | 3025074892 | 2994349007 | 4058483161 | 285021 | SRX3176099 | SRS2505862 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.93175 | 0.9329 | 0.62025 | 0.62495 | 0.96658 | 0.96739 | 0.49279 | 0.49477 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43683 | 43683 | SRR6025606 | SRX3176098 | SRS2505861 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23558 | GSM2779338 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23558 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779338 | GSM2779338: Sample 23558; Danio rerio; RNA Seq | GSM2779338 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779338 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23558_R1.fastq.gz s23558_R2.fastq.gz | fastq fastq | 13003254800.0 | 65016274.0 | GSM2779338 r1 | 0:100 1:100 | A:3758329047;C:2708543092;G:2677214324;T:3858903008;N:265329 | 100 | 100 | 3758329047 | 2708543092 | 2677214324 | 3858903008 | 265329 | SRX3176098 | SRS2505861 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.91853 | 0.91806 | 0.65078 | 0.65255 | 0.94961 | 0.95071 | 0.50517 | 0.51058 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43684 | 43684 | SRR6025605 | SRX3176097 | SRS2505860 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23557 | GSM2779337 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23557 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779337 | GSM2779337: Sample 23557; Danio rerio; RNA Seq | GSM2779337 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779337 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23557_R1.fastq.gz s23557_R2.fastq.gz | fastq fastq | 15313320600.0 | 76566603.0 | GSM2779337 r1 | 0:100 1:100 | A:4308598805;C:3312393284;G:3270540620;T:4421477194;N:310697 | 100 | 100 | 4308598805 | 3312393284 | 3270540620 | 4421477194 | 310697 | SRX3176097 | SRS2505860 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.93231 | 0.93219 | 0.77055 | 0.77158 | 0.98046 | 0.98094 | 0.56595 | 0.56298 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43685 | 43685 | SRR6025604 | SRX3176096 | SRS2505859 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23556 | GSM2779336 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23556 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779336 | GSM2779336: Sample 23556; Danio rerio; RNA Seq | GSM2779336 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779336 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23556_R1.fastq.gz s23556_R2.fastq.gz | fastq fastq | 12817928800.0 | 64089644.0 | GSM2779336 r1 | 0:100 1:100 | A:3636940808;C:2743921783;G:2720083561;T:3716727753;N:254895 | 100 | 100 | 3636940808 | 2743921783 | 2720083561 | 3716727753 | 254895 | SRX3176096 | SRS2505859 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.93256 | 0.93098 | 0.54622 | 0.54805 | 0.94541 | 0.9472 | 0.48073 | 0.47781 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43686 | 43686 | SRR6025603 | SRX3176095 | SRS2505858 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23555 | GSM2779335 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23555 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779335 | GSM2779335: Sample 23555; Danio rerio; RNA Seq | GSM2779335 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779335 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23555_R1.fastq.gz s23555_R2.fastq.gz | fastq fastq | 13164248800.0 | 65821244.0 | GSM2779335 r1 | 0:100 1:100 | A:3699423154;C:2864617193;G:2832369173;T:3767574718;N:264562 | 100 | 100 | 3699423154 | 2864617193 | 2832369173 | 3767574718 | 264562 | SRX3176095 | SRS2505858 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.93457 | 0.93477 | 0.56712 | 0.56973 | 0.95538 | 0.95635 | 0.49943 | 0.46846 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43687 | 43687 | SRR6025602 | SRX3176094 | SRS2505857 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23554 | GSM2779334 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23554 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779334 | GSM2779334: Sample 23554; Danio rerio; RNA Seq | GSM2779334 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779334 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23554_R1.fastq.gz s23554_R2.fastq.gz | fastq fastq | 7262209400.0 | 36311047.0 | GSM2779334 r1 | 0:100 1:100 | A:1907583588;C:1714326211;G:1698764389;T:1941393648;N:141564 | 100 | 100 | 1907583588 | 1714326211 | 1698764389 | 1941393648 | 141564 | SRX3176094 | SRS2505857 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.93648 | 0.9356 | 0.50734 | 0.50884 | 0.94272 | 0.94373 | 0.47032 | 0.47653 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43688 | 43688 | SRR6025601 | SRX3176093 | SRS2505856 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23553 | GSM2779333 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23553 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779333 | GSM2779333: Sample 23553; Danio rerio; RNA Seq | GSM2779333 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779333 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23553_R1.fastq.gz s23553_R2.fastq.gz | fastq fastq | 11822418400.0 | 59112092.0 | GSM2779333 r1 | 0:100 1:100 | A:3118571640;C:2785354873;G:2752046165;T:3166220124;N:225598 | 100 | 100 | 3118571640 | 2785354873 | 2752046165 | 3166220124 | 225598 | SRX3176093 | SRS2505856 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.94518 | 0.94357 | 0.55971 | 0.56137 | 0.95948 | 0.95962 | 0.45789 | 0.45663 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43689 | 43689 | SRR6025600 | SRX3176092 | SRS2505855 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23552 | GSM2779332 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23552 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779332 | GSM2779332: Sample 23552; Danio rerio; RNA Seq | GSM2779332 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779332 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23552_R1.fastq.gz s23552_R2.fastq.gz | fastq fastq | 15618525200.0 | 78092626.0 | GSM2779332 r1 | 0:100 1:100 | A:4331214340;C:3464419077;G:3419272596;T:4403312389;N:306798 | 100 | 100 | 4331214340 | 3464419077 | 3419272596 | 4403312389 | 306798 | SRX3176092 | SRS2505855 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.94354 | 0.94207 | 0.64763 | 0.64745 | 0.96765 | 0.96885 | 0.52121 | 0.50469 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43690 | 43690 | SRR6025599 | SRX3176091 | SRS2505854 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23551 | GSM2779331 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23551 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779331 | GSM2779331: Sample 23551; Danio rerio; RNA Seq | GSM2779331 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779331 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23551_R1.fastq.gz s23551_R2.fastq.gz | fastq fastq | 13523929400.0 | 67619647.0 | GSM2779331 r1 | 0:100 1:100 | A:3761044627;C:2980561485;G:2940766088;T:3841300096;N:257104 | 100 | 100 | 3761044627 | 2980561485 | 2940766088 | 3841300096 | 257104 | SRX3176091 | SRS2505854 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.93802 | 0.93656 | 0.78828 | 0.78689 | 0.97585 | 0.97617 | 0.64659 | 0.63139 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43691 | 43691 | SRR6025598 | SRX3176090 | SRS2505853 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23550 | GSM2779330 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23550 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779330 | GSM2779330: Sample 23550; Danio rerio; RNA Seq | GSM2779330 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779330 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23550_R1.fastq.gz s23550_R2.fastq.gz | fastq fastq | 13773520400.0 | 68867602.0 | GSM2779330 r1 | 0:100 1:100 | A:3781789884;C:3087914097;G:3047563316;T:3855981298;N:271805 | 100 | 100 | 3781789884 | 3087914097 | 3047563316 | 3855981298 | 271805 | SRX3176090 | SRS2505853 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.9435 | 0.94327 | 0.63355 | 0.63638 | 0.96684 | 0.96735 | 0.51875 | 0.52302 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43692 | 43692 | SRR6025597 | SRX3176089 | SRS2505852 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23549 | GSM2779329 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23549 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779329 | GSM2779329: Sample 23549; Danio rerio; RNA Seq | GSM2779329 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779329 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23549_R1.fastq.gz s23549_R2.fastq.gz | fastq fastq | 13833565400.0 | 69167827.0 | GSM2779329 r1 | 0:100 1:100 | A:3871499806;C:3039772666;G:2996616126;T:3925408591;N:268211 | 100 | 100 | 3871499806 | 3039772666 | 2996616126 | 3925408591 | 268211 | SRX3176089 | SRS2505852 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.93554 | 0.93467 | 0.54178 | 0.54255 | 0.95156 | 0.95177 | 0.53446 | 0.54157 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43693 | 43693 | SRR6025596 | SRX3176088 | SRS2505851 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23548 | GSM2779328 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23548 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779328 | GSM2779328: Sample 23548; Danio rerio; RNA Seq | GSM2779328 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779328 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23548_R1.fastq.gz s23548_R2.fastq.gz | fastq fastq | 13820952200.0 | 69104761.0 | GSM2779328 r1 | 0:100 1:100 | A:3860273103;C:3045401890;G:2998258507;T:3916751954;N:266746 | 100 | 100 | 3860273103 | 3045401890 | 2998258507 | 3916751954 | 266746 | SRX3176088 | SRS2505851 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.93826 | 0.93761 | 0.62803 | 0.62906 | 0.95913 | 0.96004 | 0.5438 | 0.54591 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43694 | 43694 | SRR6025595 | SRX3176087 | SRS2505850 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23547 | GSM2779327 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23547 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779327 | GSM2779327: Sample 23547; Danio rerio; RNA Seq | GSM2779327 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779327 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23547_R1.fastq.gz s23547_R2.fastq.gz | fastq fastq | 11366785600.0 | 56833928.0 | GSM2779327 r1 | 0:100 1:100 | A:3214019580;C:2456125449;G:2428331610;T:3268085490;N:223471 | 100 | 100 | 3214019580 | 2456125449 | 2428331610 | 3268085490 | 223471 | SRX3176087 | SRS2505850 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.92317 | 0.92291 | 0.5299 | 0.53266 | 0.94113 | 0.94217 | 0.51651 | 0.52118 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43695 | 43695 | SRR6025594 | SRX3176086 | SRS2505849 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23546 | GSM2779326 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23546 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779326 | GSM2779326: Sample 23546; Danio rerio; RNA Seq | GSM2779326 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779326 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23546_R1.fastq.gz s23546_R2.fastq.gz | fastq fastq | 12174866600.0 | 60874333.0 | GSM2779326 r1 | 0:100 1:100 | A:3452417750;C:2615757090;G:2585494526;T:3520960685;N:236549 | 100 | 100 | 3452417750 | 2615757090 | 2585494526 | 3520960685 | 236549 | SRX3176086 | SRS2505849 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.92674 | 0.9259 | 0.59418 | 0.5966 | 0.9526 | 0.95408 | 0.47877 | 0.4871 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43696 | 43696 | SRR6025593 | SRX3176085 | SRS2505848 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23545 | GSM2779325 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23545 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779325 | GSM2779325: Sample 23545; Danio rerio; RNA Seq | GSM2779325 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779325 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23545_R1.fastq.gz s23545_R2.fastq.gz | fastq fastq | 12332102000.0 | 61660510.0 | GSM2779325 r1 | 0:100 1:100 | A:3455012273;C:2700750069;G:2667784512;T:3508316711;N:238435 | 100 | 100 | 3455012273 | 2700750069 | 2667784512 | 3508316711 | 238435 | SRX3176085 | SRS2505848 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.93462 | 0.93428 | 0.44648 | 0.45292 | 0.94397 | 0.94491 | 0.48987 | 0.49012 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43697 | 43697 | SRR6025592 | SRX3176084 | SRS2505847 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23544 | GSM2779324 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23544 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779324 | GSM2779324: Sample 23544; Danio rerio; RNA Seq | GSM2779324 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779324 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23544_R1.fastq.gz s23544_R2.fastq.gz | fastq fastq | 11495965400.0 | 57479827.0 | GSM2779324 r1 | 0:100 1:100 | A:3239277586;C:2499452258;G:2466282264;T:3290731467;N:221825 | 100 | 100 | 3239277586 | 2499452258 | 2466282264 | 3290731467 | 221825 | SRX3176084 | SRS2505847 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.92887 | 0.92785 | 0.50244 | 0.50529 | 0.94379 | 0.94406 | 0.47153 | 0.47993 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43698 | 43698 | SRR6025591 | SRX3176083 | SRS2505846 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 23543 | GSM2779323 | tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 23543 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779323 | GSM2779323: Sample 23543; Danio rerio; RNA Seq | GSM2779323 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779323 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s23543_R1.fastq.gz s23543_R2.fastq.gz | fastq fastq | 12269933200.0 | 61349666.0 | GSM2779323 r1 | 0:100 1:100 | A:3285868097;C:2845990394;G:2808031165;T:3329810665;N:232879 | 100 | 100 | 3285868097 | 2845990394 | 2808031165 | 3329810665 | 232879 | SRX3176083 | SRS2505846 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.94094 | 0.94004 | 0.54712 | 0.54678 | 0.95444 | 0.95491 | 0.50258 | 0.51231 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43699 | 43699 | SRR6025590 | SRX3176082 | SRS2505845 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 20599 | GSM2779322 | tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 20599 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779322 | GSM2779322: Sample 20599; Danio rerio; RNA Seq | GSM2779322 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779322 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | loader:fastq load.py | s20599_R1.fastq.gz s20599_R2.fastq.gz | fastq fastq | 13570689150.0 | 64830571.0 | GSM2779322 r1 | 0:104.66 1:104.66 | A:3746382385;C:3035431532;G:3017617207;T:3766655416;N:4602610 | 104 | 104 | 3746382385 | 3035431532 | 3017617207 | 3766655416 | 4602610 | SRX3176082 | SRS2505845 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.68337 | 0.68693 | 0.21707 | 0.22287 | 0.9598 | 0.96112 | 0.49497 | 0.51067 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||
| 43700 | 43700 | SRR6025589 | SRX3176081 | SRS2505844 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 20595 | GSM2779321 | tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 20595 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779321 | GSM2779321: Sample 20595; Danio rerio; RNA Seq | GSM2779321 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779321 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | loader:fastq load.py | s20595_R1.fastq.gz s20595_R2.fastq.gz | fastq fastq | 11070127350.0 | 52852383.0 | GSM2779321 r1 | 0:104.73 1:104.73 | A:2982708297;C:2554784552;G:2519746253;T:3009345413;N:3542835 | 104 | 104 | 2982708297 | 2554784552 | 2519746253 | 3009345413 | 3542835 | SRX3176081 | SRS2505844 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.60906 | 0.61457 | 0.36125 | 0.3667 | 0.9582 | 0.96059 | 0.51449 | 0.50705 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||
| 43701 | 43701 | SRR6025588 | SRX3176080 | SRS2505843 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 20566 | GSM2779320 | tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 20566 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779320 | GSM2779320: Sample 20566; Danio rerio; RNA Seq | GSM2779320 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779320 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | loader:fastq load.py | s20566_R1.fastq.gz s20566_R2.fastq.gz | fastq fastq | 13606761150.0 | 65046784.0 | GSM2779320 r1 | 0:104.59 1:104.59 | A:3665640421;C:3135272778;G:3111565962;T:3689671946;N:4610043 | 104 | 104 | 3665640421 | 3135272778 | 3111565962 | 3689671946 | 4610043 | SRX3176080 | SRS2505843 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.66341 | 0.66751 | 0.25233 | 0.25854 | 0.95696 | 0.9587 | 0.49264 | 0.50014 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||
| 43702 | 43702 | SRR6025587 | SRX3176079 | SRS2505841 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 20565 | GSM2779319 | tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 20565 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779319 | GSM2779319: Sample 20565; Danio rerio; RNA Seq | GSM2779319 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779319 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | loader:fastq load.py | s20565_R1.fastq.gz s20565_R2.fastq.gz | fastq fastq | 13510104100.0 | 64509618.0 | GSM2779319 r1 | 0:104.71 1:104.71 | A:3690515096;C:3059445453;G:3040155086;T:3715724132;N:4264333 | 104 | 104 | 3690515096 | 3059445453 | 3040155086 | 3715724132 | 4264333 | SRX3176079 | SRS2505841 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.67247 | 0.67728 | 0.30104 | 0.30816 | 0.95753 | 0.95868 | 0.50785 | 0.50355 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||
| 43703 | 43703 | SRR6025586 | SRX3176078 | SRS2505842 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 20556 | GSM2779318 | tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 20556 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779318 | GSM2779318: Sample 20556; Danio rerio; RNA Seq | GSM2779318 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779318 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | loader:fastq load.py | s20556_R1.fastq.gz s20556_R2.fastq.gz | fastq fastq | 12979896450.0 | 61997072.0 | GSM2779318 r1 | 0:104.68 1:104.68 | A:3360577219;C:3127516743;G:3108274254;T:3379692612;N:3835622 | 104 | 104 | 3360577219 | 3127516743 | 3108274254 | 3379692612 | 3835622 | SRX3176078 | SRS2505842 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.71027 | 0.71422 | 0.16443 | 0.16968 | 0.94688 | 0.94771 | 0.45596 | 0.466 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||
| 43704 | 43704 | SRR6025585 | SRX3176077 | SRS2505840 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 20545 | GSM2779317 | tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 20545 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779317 | GSM2779317: Sample 20545; Danio rerio; RNA Seq | GSM2779317 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779317 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | loader:fastq load.py | s20545_R1.fastq.gz s20545_R2.fastq.gz | fastq fastq | 12989935500.0 | 62257631.0 | GSM2779317 r1 | 0:104.32 1:104.32 | A:3572227261;C:2914841466;G:2894234446;T:3604038426;N:4593901 | 104 | 104 | 3572227261 | 2914841466 | 2894234446 | 3604038426 | 4593901 | SRX3176077 | SRS2505840 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.68046 | 0.68257 | 0.24349 | 0.25017 | 0.96098 | 0.96146 | 0.49722 | 0.49929 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||
| 43705 | 43705 | SRR6025584 | SRX3176076 | SRS2505838 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 20544 | GSM2779316 | tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 20544 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779316 | GSM2779316: Sample 20544; Danio rerio; RNA Seq | GSM2779316 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779316 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | loader:fastq load.py | s20544_R1.fastq.gz s20544_R2.fastq.gz | fastq fastq | 10850415100.0 | 51845962.0 | GSM2779316 r1 | 0:104.64 1:104.64 | A:2883478486;C:2540887534;G:2532673572;T:2889737674;N:3637834 | 104 | 104 | 2883478486 | 2540887534 | 2532673572 | 2889737674 | 3637834 | SRX3176076 | SRS2505838 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.75352 | 0.75587 | 0.27675 | 0.2836 | 0.94454 | 0.9455 | 0.4848 | 0.48686 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||
| 43706 | 43706 | SRR6025583 | SRX3176075 | SRS2505839 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 20535 | GSM2779315 | tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 20535 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779315 | GSM2779315: Sample 20535; Danio rerio; RNA Seq | GSM2779315 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779315 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | loader:fastq load.py | s20535_R1.fastq.gz s20535_R2.fastq.gz | fastq fastq | 11095624100.0 | 53041376.0 | GSM2779315 r1 | 0:104.59 1:104.59 | A:2935149963;C:2612483606;G:2588444487;T:2955689662;N:3856382 | 104 | 104 | 2935149963 | 2612483606 | 2588444487 | 2955689662 | 3856382 | SRX3176075 | SRS2505839 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.66175 | 0.66467 | 0.28361 | 0.28982 | 0.95446 | 0.95637 | 0.4427 | 0.46855 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||
| 43707 | 43707 | SRR6025582 | SRX3176074 | SRS2505837 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 20534 | GSM2779314 | tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 20534 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779314 | GSM2779314: Sample 20534; Danio rerio; RNA Seq | GSM2779314 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779314 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | loader:fastq load.py | s20534_R1.fastq.gz s20534_R2.fastq.gz | fastq fastq | 9279270400.0 | 44312137.0 | GSM2779314 r1 | 0:104.70 1:104.70 | A:2257778518;C:2383104726;G:2364686021;T:2270914797;N:2786338 | 104 | 104 | 2257778518 | 2383104726 | 2364686021 | 2270914797 | 2786338 | SRX3176074 | SRS2505837 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.75658 | 0.75749 | 0.03939 | 0.03975 | 0.95465 | 0.95633 | 0.43347 | 0.45305 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||
| 43708 | 43708 | SRR6025581 | SRX3176073 | SRS2505836 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 18931 | GSM2779313 | tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 18931 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779313 | GSM2779313: Sample 18931; Danio rerio; RNA Seq | GSM2779313 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779313 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s18931_R2.fastq.gz s18931_R1.fastq.gz | fastq fastq | 10382332600.0 | 51911663.0 | GSM2779313 r1 | 0:100 1:100 | A:2908734493;C:2273168729;G:2245788132;T:2952822006;N:1819240 | 100 | 100 | 2908734493 | 2273168729 | 2245788132 | 2952822006 | 1819240 | SRX3176073 | SRS2505836 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.67976 | 0.68217 | 0.31458 | 0.31819 | 0.95726 | 0.95763 | 0.48306 | 0.47976 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43709 | 43709 | SRR6025580 | SRX3176072 | SRS2505835 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 18930 | GSM2779312 | tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 18930 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779312 | GSM2779312: Sample 18930; Danio rerio; RNA Seq | GSM2779312 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779312 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s18930_R1.fastq.gz s18930_R2.fastq.gz | fastq fastq | 13527577200.0 | 67637886.0 | GSM2779312 r1 | 0:100 1:100 | A:3738123002;C:3017390941;G:2980829526;T:3788876926;N:2356805 | 100 | 100 | 3738123002 | 3017390941 | 2980829526 | 3788876926 | 2356805 | SRX3176072 | SRS2505835 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.72022 | 0.72046 | 0.30139 | 0.30255 | 0.94679 | 0.94744 | 0.48588 | 0.48782 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43710 | 43710 | SRR6025579 | SRX3176071 | SRS2505834 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 18928 | GSM2779311 | tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 18928 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779311 | GSM2779311: Sample 18928; Danio rerio; RNA Seq | GSM2779311 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779311 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s18928_R1.fastq.gz s18928_R2.fastq.gz | fastq fastq | 11247464600.0 | 56237323.0 | GSM2779311 r1 | 0:100 1:100 | A:3119559722;C:2500776647;G:2474446157;T:3150698487;N:1983587 | 100 | 100 | 3119559722 | 2500776647 | 2474446157 | 3150698487 | 1983587 | SRX3176071 | SRS2505834 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.645 | 0.64814 | 0.2583 | 0.26292 | 0.95741 | 0.9586 | 0.47386 | 0.48835 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43711 | 43711 | SRR6025578 | SRX3176070 | SRS2505833 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 18927 | GSM2779310 | tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 18927 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779310 | GSM2779310: Sample 18927; Danio rerio; RNA Seq | GSM2779310 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779310 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s18927_R1.fastq.gz s18927_R2.fastq.gz | fastq fastq | 10683045600.0 | 53415228.0 | GSM2779310 r1 | 0:100 1:100 | A:2868542756;C:2476008591;G:2434571227;T:2902046467;N:1876559 | 100 | 100 | 2868542756 | 2476008591 | 2434571227 | 2902046467 | 1876559 | SRX3176070 | SRS2505833 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.55065 | 0.55754 | 0.24721 | 0.25312 | 0.96883 | 0.96978 | 0.5382 | 0.5322 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||
| 43712 | 43712 | SRR6025577 | SRX3176069 | SRS2505832 | SRP117248 | PRJNA404067 | Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation | GSE103692 | Transcriptome Analysis | We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500 | pubmed:29385124 | Sample 18926 | GSM2779309 | tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | Sample 18926 | Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements | OMP positive cell | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit | GSM2779309 | GSM2779309: Sample 18926; Danio rerio; RNA Seq | GSM2779309 | 1 | Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit | GEO Accession:GSM2779309 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP117248 | s18926_R1.fastq.gz s18926_R2.fastq.gz | fastq fastq | 9785632200.0 | 48928161.0 | GSM2779309 r1 | SRX3176069 | SRS2505832 | SRA606958 | GEO | Junhyong Kim, Biology, University of Pennsylvania | 2 | 0.56035 | 0.54079 | 0.19973 | 0.19425 | 0.95905 | 0.95988 | 0.50309 | 0.50507 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | smarter | sc | single_cell_plate | fluidigm | United States | 2017-09-11 | Undetermined | Undetermined | Undetermined | Undetermined |
Advanced export
JSON shape: default, array, newline-delimited
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");;