RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

87 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" and tissue_curation_coarse = "Surface Structure"

✎ View and edit SQL

This data as json, CSV (advanced)

devstage_curation 6

tissue_curation 4

devstage_curation_coarse 4

experiment.library_strategy 2

experiment.library_selection 2

tissue_curation_coarse 1

  • Surface Structure · 87 ✖

technology 1

  • 10x · 87 ✖

experiment.platform 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 87 ✖

experiment.library_layout 1

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
43983 43983 SRR6811832 SRX3768872 SRS3023386 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva F1 2 scar GSM3032175   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva F1 2 scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM3032175 GSM3032175: Larva F1 2 scar; Danio rerio; OTHER GSM3032175   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032175 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     F1_2_scar_R1.fastq.gz F1_2_scar_R2.fastq.gz fastq fastq 9301928572.0 75015553.0 GSM3032175 r1 0:26 1:98 A:2682085389;C:3008788535;G:2093169318;T:1516220703;N:1664627 26 98     2682085389 3008788535 2093169318 1516220703 1664627 SRX3768872 SRS3023386 SRA623333 GEO Max Delbrück Center 2 0.0001 0.00173 4e-05 8e-05 0.99983 0.99667 0.33333 0.531 26 98 T T mates < 9% mapping rate illumina hiseq_era unknown other unknown sc single_cell_droplet 10x   Germany 2018-03-06 Larval Larval Trunk Surface Structure
43984 43984 SRR6811831 SRX3768871 SRS3023388 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva F1 1 scar GSM3032174   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva F1 1 scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM3032174 GSM3032174: Larva F1 1 scar; Danio rerio; OTHER GSM3032174   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032174 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     F1_1_scar_R1.fastq.gz F1_1_scar_R2.fastq.gz fastq fastq 7772713576.0 62683174.0 GSM3032174 r1 0:26 1:98 A:2222016153;C:2555237987;G:1722216404;T:1271855931;N:1387101 26 98     2222016153 2555237987 1722216404 1271855931 1387101 SRX3768871 SRS3023388 SRA623333 GEO Max Delbrück Center 2 0.00014 0.00171 8e-05 0.00012 0.99985 0.99642 0.44444 0.45454 26 98 T T mates < 9% mapping rate illumina hiseq_era unknown other unknown sc single_cell_droplet 10x   Germany 2018-03-06 Larval Larval Trunk Surface Structure
43985 43985 SRR6811830 SRX3768870 SRS3023387 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva F1 2 mRNA GSM3032173   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva F1 2 mRNA Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes. Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM3032173 GSM3032173: Larva F1 2 mRNA; Danio rerio; RNA Seq GSM3032173   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032173 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     F1_2_wt_R1.fastq.gz F1_2_wt_R2.fastq.gz fastq fastq 29997480708.0 241915167.0 GSM3032173 r1 0:26 1:98 A:8264355452;C:6830431714;G:7093261338;T:7804053400;N:5378804 26 98     8264355452 6830431714 7093261338 7804053400 5378804 SRX3768870 SRS3023387 SRA623333 GEO Max Delbrück Center 2 0.00307 0.94486 0.00051 0.08199 0.99431 0.82509 0.36875 0.43599 26 98 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2018-03-06 Larval Larval Trunk Surface Structure
43986 43986 SRR6811829 SRX3768869 SRS3023385 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva F1 1 mRNA GSM3032172   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva F1 1 mRNA Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes. Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM3032172 GSM3032172: Larva F1 1 mRNA; Danio rerio; RNA Seq GSM3032172   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032172 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     F1_1_wt_R1.fastq.gz F1_1_wt_R2.fastq.gz fastq fastq 26685876072.0 215208678.0 GSM3032172 r1 0:26 1:98 A:7365353958;C:6068313931;G:6251004125;T:6996410946;N:4793112 26 98     7365353958 6068313931 6251004125 6996410946 4793112 SRX3768869 SRS3023385 SRA623333 GEO Max Delbrück Center 2 0.00255 0.93758 0.00046 0.08179 0.99515 0.82637 0.35368 0.46605 26 98 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2018-03-06 Larval Larval Trunk Surface Structure
43991 43991 SRR6811824 SRX3768864 SRS3023381 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva 5 scar GSM3032167   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva 5 scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM3032167 GSM3032167: Larva 5 scar; Danio rerio; OTHER GSM3032167   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032167 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     Z5_scar_R1.fastq.gz Z5_scar_R2.fastq.gz fastq fastq 7672645700.0 61876175.0 GSM3032167 r1 0:26 1:98 A:2173948352;C:2439410929;G:1714624642;T:1343296377;N:1365400 26 98     2173948352 2439410929 1714624642 1343296377 1365400 SRX3768864 SRS3023381 SRA623333 GEO Max Delbrück Center 2 0.00013 0.00164 9e-05 8e-05 0.99989 0.99669 0.83333 0.4918 26 98 T T mates < 9% mapping rate illumina hiseq_era unknown other unknown sc single_cell_droplet 10x   Germany 2018-03-06 Larval Larval Trunk Surface Structure
43992 43992 SRR6811823 SRX3768863 SRS3023380 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva 4 scar GSM3032166   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva 4 scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM3032166 GSM3032166: Larva 4 scar; Danio rerio; OTHER GSM3032166   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032166 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     Z4_scar_R1.fastq.gz Z4_scar_R2.fastq.gz fastq fastq 7236183804.0 58356321.0 GSM3032166 r1 0:26 1:98 A:2080254513;C:2296727471;G:1625115068;T:1232786300;N:1300452 26 98     2080254513 2296727471 1625115068 1232786300 1300452 SRX3768863 SRS3023380 SRA623333 GEO Max Delbrück Center 2 0.00014 0.0016 0.00011 7e-05 0.99993 0.99634 0.33333 0.46694 26 98 T T mates < 9% mapping rate illumina hiseq_era unknown other unknown sc single_cell_droplet 10x   Germany 2018-03-06 Larval Larval Trunk Surface Structure
43997 43997 SRR6811818 SRX3768858 SRS3023376 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva 5 mRNA GSM3032161   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva 5 mRNA Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes. Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM3032161 GSM3032161: Larva 5 mRNA; Danio rerio; RNA Seq GSM3032161   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032161 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     Z5_wt_R1.fastq.gz Z5_wt_R2.fastq.gz fastq fastq 27409556812.0 221044813.0 GSM3032161 r1 0:26 1:98 A:7637677199;C:6210942203;G:6438364980;T:7117667800;N:4904630 26 98     7637677199 6210942203 6438364980 7117667800 4904630 SRX3768858 SRS3023376 SRA623333 GEO Max Delbrück Center 2 0.00523 0.92734 0.0008 0.0687 0.98916 0.81479 0.44117 0.50243 26 98 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2018-03-06 Larval Larval Trunk Surface Structure
43998 43998 SRR6811817 SRX3768857 SRS3023374 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva 4 mRNA GSM3032160   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva 4 mRNA Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes. Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM3032160 GSM3032160: Larva 4 mRNA; Danio rerio; RNA Seq GSM3032160   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032160 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     Z4_wt_R2.fastq.gz Z4_wt_R1.fastq.gz fastq fastq 19775711456.0 159481544.0 GSM3032160 r1 0:26 1:98 A:5483727144;C:4548396363;G:4737957565;T:5002119078;N:3511306 26 98     5483727144 4548396363 4737957565 5002119078 3511306 SRX3768857 SRS3023374 SRA623333 GEO Max Delbrück Center 2 0.00331 0.93006 0.00057 0.05973 0.99253 0.82369 0.38666 0.48899 26 98 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2018-03-06 Larval Larval Trunk Surface Structure
43999 43999 SRR6811816 SRX3768856 SRS3023373 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva 3 mRNA GSM3032159   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva 3 mRNA Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes. Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM3032159 GSM3032159: Larva 3 mRNA; Danio rerio; RNA Seq GSM3032159   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032159 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     Z3_wt_R1.fastq.gz Z3_wt_R2.fastq.gz Z3_wt_R3.fastq.gz fastq fastq fastq 8016913120.0 50105707.0 GSM3032159 r1 0:130 1:14 2:16 A:2047850756;C:1318672327;G:1403772432;T:1743394108;N:52287 130 14 16   2047850756 1318672327 1403772432 1743394108 52287 SRX3768856 SRS3023373 SRA623333 GEO Max Delbrück Center 1 0.87661   0.06466   0.86614   0.53364   130   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2018-03-06 Larval Larval Trunk Surface Structure
44005 44005 SRR6211487 SRX3320762 SRS2626335 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva 2 mRNA GSM2830057   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva 2 mRNA Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode a UMI and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode we counted the number of molecules mapped to each gene using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t = K ln1 – k o/K with t the final number of transcripts k o the observed UMIs and K the total number of UMIs possible. As protection against barcode sequencing errors we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes. Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM2830057 GSM2830057: Larva 2 mRNA; Danio rerio; RNA Seq GSM2830057   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM2830057 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     Z1_wt_R3.fastq.gz Z1_wt_R2.fastq.gz Z1_wt_R1.fastq.gz fastq fastq fastq 28368351950.0 232527475.0 GSM2830057 r1 0:98 1:14 2:10 A:6582076349;C:4985163175;G:5131319282;T:6085835988;N:3297756 98 14 10   6582076349 4985163175 5131319282 6085835988 3297756 SRX3320762 SRS2626335 SRA623333 GEO Max Delbrück Center 1 0.9378   0.05825   0.79687   0.50342   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2017-10-24 Larval Larval Trunk Surface Structure
44006 44006 SRR6211485 SRX3320760 SRS2626333 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva 1 mRNA GSM2830056   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva 1 mRNA Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode a UMI and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode we counted the number of molecules mapped to each gene using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t = K ln1 – k o/K with t the final number of transcripts k o the observed UMIs and K the total number of UMIs possible. As protection against barcode sequencing errors we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes. Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM2830056 GSM2830056: Larva 1 mRNA; Danio rerio; RNA Seq GSM2830056   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM2830056 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     Z2_1_wt_R1.fastq.gz Z2_1_wt_R2.fastq.gz Z2_1_wt_R3.fastq.gz fastq fastq fastq 36065037280.0 225406483.0 GSM2830056 r1 0:130 1:14 2:16 A:9121762570;C:5889322717;G:6251660049;T:8039869338;N:228116 130 14 16   9121762570 5889322717 6251660049 8039869338 228116 SRX3320760 SRS2626333 SRA623333 GEO Max Delbrück Center 1 0.88569   0.08353   0.86016   0.53379   130   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2017-10-24 Larval Larval Trunk Surface Structure
44007 44007 SRR6211486 SRX3320760 SRS2626333 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva 1 mRNA GSM2830056   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva 1 mRNA Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode a UMI and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode we counted the number of molecules mapped to each gene using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t = K ln1 – k o/K with t the final number of transcripts k o the observed UMIs and K the total number of UMIs possible. As protection against barcode sequencing errors we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes. Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM2830056 GSM2830056: Larva 1 mRNA; Danio rerio; RNA Seq GSM2830056   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM2830056 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     Z2_2_wt_R1.fastq.gz Z2_2_wt_R2.fastq.gz Z2_2_wt_R3.fastq.gz fastq fastq fastq 7700646560.0 48129041.0 GSM2830056 r2 0:130 1:14 2:16 A:1890861891;C:1307860042;G:1403340071;T:1654667424;N:45902 130 14 16   1890861891 1307860042 1403340071 1654667424 45902 SRX3320760 SRS2626333 SRA623333 GEO Max Delbrück Center 1 0.89198   0.07477   0.87288   0.49519   130   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2017-10-24 Larval Larval Trunk Surface Structure
44013 44013 SRR6211477 SRX3320753 SRS2626327 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva 1 scar GSM2830049   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva 1 scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM2830049 GSM2830049: Larva 1 scar; Danio rerio; OTHER GSM2830049   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM2830049 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     Z2_1_scar_R1.fastq.gz Z2_1_scar_R2.fastq.gz Z2_1_scar_R3.fastq.gz fastq fastq fastq 1358915680.0 8493223.0 GSM2830049 r1 0:130 1:14 2:16 A:286107087;C:390283378;G:268551180;T:159171790;N:5555 130 14 16   286107087 390283378 268551180 159171790 5555 SRX3320753 SRS2626327 SRA623333 GEO Max Delbrück Center 1 0.00515   8e-05   0.99959   0.24561   130   T   under 1.2% mapping rate illumina hiseq_era unknown other unknown sc single_cell_droplet 10x   Germany 2017-10-24 Larval Larval Trunk Surface Structure
44014 44014 SRR6211478 SRX3320753 SRS2626327 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva 1 scar GSM2830049   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva 1 scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM2830049 GSM2830049: Larva 1 scar; Danio rerio; OTHER GSM2830049   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM2830049 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     Z2_2_scar_R1.fastq.gz Z2_2_scar_R2.fastq.gz Z2_2_scar_R3.fastq.gz fastq fastq fastq 1103410080.0 6896313.0 GSM2830049 r2 0:130 1:14 2:16 A:232542409;C:315925727;G:218437491;T:129610895;N:4168 130 14 16   232542409 315925727 218437491 129610895 4168 SRX3320753 SRS2626327 SRA623333 GEO Max Delbrück Center 1 0.00786   0.0   0.99922   0.31764   130   T   under 1.2% mapping rate illumina hiseq_era unknown other unknown sc single_cell_droplet 10x   Germany 2017-10-24 Larval Larval Trunk Surface Structure
52209 52209 SRR8992787 SRX5771765 SRS4705624 SRP194294 PRJNA540521 Fate plasticity and reprogramming in genetically distinct populations of Danio leucophores GSE130526 Other Understanding genetic and cellular bases of adult form remains a fundamental goal at the intersection of developmental and evolutionary biology. The skin pigment cells of vertebrates derived from embryonic neural crest are a useful system for elucidating mechanisms of fate specification pattern formation and how particular phenotypes impact organismal behavior and ecology. In a survey of Danio fishes including zebrafish Danio rerio we identified two populations of white pigment cells—leucophores—one of which arises by transdifferentiation of adult melanophores and another that develops from a yellow/orange xanthophore like progenitor. Single cell transcriptomic mutational chemical and ultrastructural analyses of zebrafish leucophores revealed cell type specific chemical compositions organelle configurations and genetic requirements. At the organismal level we identified distinct physiological responses of leucophores during environmental background matching and we show that leucophore complement influences behavior. Together our studies revealed new independently arisen pigment cell types and mechanisms of fate acquisition in zebrafish and illustrate how concerted analyses across hierarchical levels can provide insights into phenotypes and their evolution. Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform using zebrafish fin pigment cells FACs sorted for mCherry. For additional details see associated publication   pubmed:31138706   Zebrafish fin pigment cells GSM3741778   tissue:Dorsal and anal fins|cell type:pigment cells|treatment:Untreated Zebrafish fin pigment cells Expression matrix files were generated using cellranger 10X genomics version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Genome build: GRCz11/danRer11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. Dorsal and anal fins Fins were amputated from fish expressing both pnp4a:palmmCherry and tyrp1b:palmmCherry. To approximately normalize capture of relevant cell types by quantity and improve the likelihood of recovering cells at intermediate states of differentiation we extracted distal dorsal fin regions 10 mm standard length SL; n=20 and proximal interstripe anal fin regions 14 mm SL; n=10. Tissue was enzymatically dissociated with Liberase 0.25 mg/mL in dPBS at 25°C for 15 min followed by manual trituration with a flame polished glass pipette for 5 min. Cell suspensions were then filtered through a 70 μm Nylon cell strainer to obtain a single cell suspension. Liberated cells were re suspended in 1% BSA / 5% FBS in dPBS and DAPI 0.1 μg/mL 15 min before FACS purification. All plastic and glass surfaces of cell contact were coated with 1% BSA in dPBS before to use. Prior to sorting for fluorescence levels single cells were isolated by sequentially gating cells according to their SSC A vs. FSC A FSC H vs FSC W and SSC H vs SSC W profiles according to standard flow cytometry practices. Cells with high levels of DAPI staining were excluded as dead or damaged. Cells from wild type zebrafish were used as negative control to determine gates for detection of mCherry and GFP fluorescence and then cells from transgenic fish were purified according to these gates. All samples were kept on ice except during Liberase incubation and then sorted chilled. 10X genomics V1 protocol following manufacturer recommendations. Fish were maintained at 28.5C with 10 h : 14 h light:dark conditions. Larvae were reared with marine rotifers supplemented with Artemac Aquafauna followed by Artemia and flake food. Adults were maintained on Artemia and flake food. Fish stocks of Danio rerio: WTABb a derivative of inbred ABwp Tgtyrp1b:palm mCherrywp.rt11 Tgpnp4a:palmmCherrywp.rt10 cell type:pigment cells|treatment:Untreated GSM3741778 GSM3741778: Zebrafish fin pigment cells; Danio rerio; RNA Seq GSM3741778   1 10X genomics V1 protocol following manufacturer recommendations.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP194294     leucophore_S9_L003_R2_001.fastq.gz leucophore_S9_L004_R1_001.fastq.gz fastq fastq 424061944.0 10241510.0 GSM3741778 r1 0:26 1:57 A:119042142;C:89897538;G:98172861;T:116716009;N:233394 26 57     119042142 89897538 98172861 116716009 233394 SRX5771765 SRS4705624 SRA881136 GEO Parichy Lab, Biology, University of Washington 1 0.33934   0.07693   0.8742   0.51425   57   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-04-30 Multi-stage Multi-stage Fin Surface Structure
52244 52244 SRR9050631 SRX5827022 SRS4754836 SRP198298 PRJNA542704 Thyroid hormone regulates distinct paths to maturation in pigment cell lineages GSE131136 Transcriptome Analysis Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.   pubmed:31140974;pubmed:33933422   Neural crest derived cells from hypothyroid post embryonic zebrafish trunks biological replicate 7 GSM3764578   tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:2650 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid Neural crest derived cells from hypothyroid post embryonic zebrafish trunks biological replicate 7 Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. sox10:Cre+ cells from post embryonic zebrafish trunk tissue Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms. cell type:2650 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid GSM3764578 GSM3764578: Neural crest derived cells from hypothyroid post embryonic zebrafish trunks biological replicate 7; Danio rerio; RNA Seq GSM3764578   1 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP198298   dangling references:treat as unmapped hypo5_possorted_genome_bam.bam 10X Genomics bam file 6174558858.0 108325594.0 GSM3764578 r1 0:57 A:1897524564;C:1180297377;G:1360942367;T:1732425907;N:3368643 57       1897524564 1180297377 1360942367 1732425907 3368643 SRX5827022 SRS4754836 SRA886020 GEO Biology, University of Virginia 1 0.91289   0.25388   0.82856   0.50847   57   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-05-13 Larval Larval Trunk Surface Structure
52245 52245 SRR9050630 SRX5827021 SRS4754835 SRP198298 PRJNA542704 Thyroid hormone regulates distinct paths to maturation in pigment cell lineages GSE131136 Transcriptome Analysis Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.   pubmed:31140974;pubmed:33933422   Neural crest derived cells from hypothyroid post embryonic zebrafish trunks biological replicate 6 GSM3764577   tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:1888 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid Neural crest derived cells from hypothyroid post embryonic zebrafish trunks biological replicate 6 Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. sox10:Cre+ cells from post embryonic zebrafish trunk tissue Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms. cell type:1888 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid GSM3764577 GSM3764577: Neural crest derived cells from hypothyroid post embryonic zebrafish trunks biological replicate 6; Danio rerio; RNA Seq GSM3764577   1 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP198298   dangling references:treat as unmapped hypo4_possorted_genome_bam.bam 10X Genomics bam file 4410277587.0 77373291.0 GSM3764577 r1 0:57 A:1320513576;C:874241368;G:1044266437;T:1169033783;N:2222423 57       1320513576 874241368 1044266437 1169033783 2222423 SRX5827021 SRS4754835 SRA886020 GEO Biology, University of Virginia 1 0.92536   0.20155   0.83473   0.50983   57   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-05-13 Larval Larval Trunk Surface Structure
52246 52246 SRR9050629 SRX5827020 SRS4754834 SRP198298 PRJNA542704 Thyroid hormone regulates distinct paths to maturation in pigment cell lineages GSE131136 Transcriptome Analysis Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.   pubmed:31140974;pubmed:33933422   Neural crest derived cells from hypothyroid post embryonic zebrafish trunks biological replicate 5 GSM3764576   tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:774 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid Neural crest derived cells from hypothyroid post embryonic zebrafish trunks biological replicate 5 Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. sox10:Cre+ cells from post embryonic zebrafish trunk tissue Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms. cell type:774 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid GSM3764576 GSM3764576: Neural crest derived cells from hypothyroid post embryonic zebrafish trunks biological replicate 5; Danio rerio; RNA Seq GSM3764576   1 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP198298   dangling references:treat as unmapped hypo3_possorted_genome_bam.bam 10X Genomics bam file 8444232738.0 148144434.0 GSM3764576 r1 0:57 A:2380116568;C:1626615273;G:2248860789;T:2185343861;N:3296247 57       2380116568 1626615273 2248860789 2185343861 3296247 SRX5827020 SRS4754834 SRA886020 GEO Biology, University of Virginia 1 0.91177   0.16393   0.80509   0.514   57   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-05-13 Larval Larval Trunk Surface Structure
52247 52247 SRR9050628 SRX5827019 SRS4754833 SRP198298 PRJNA542704 Thyroid hormone regulates distinct paths to maturation in pigment cell lineages GSE131136 Transcriptome Analysis Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.   pubmed:31140974;pubmed:33933422   Neural crest derived cells from hypothyroid post embryonic zebrafish trunks biological replicate 4 GSM3764575   tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:941 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid Neural crest derived cells from hypothyroid post embryonic zebrafish trunks biological replicate 4 Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. sox10:Cre+ cells from post embryonic zebrafish trunk tissue Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms. cell type:941 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid GSM3764575 GSM3764575: Neural crest derived cells from hypothyroid post embryonic zebrafish trunks biological replicate 4; Danio rerio; RNA Seq GSM3764575   1 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP198298   dangling references:treat as unmapped hypo2_possorted_genome_bam.bam 10X Genomics bam file 8711801454.0 152838622.0 GSM3764575 r1 0:57 A:2469579044;C:1654897730;G:2303443265;T:2280478208;N:3403207 57       2469579044 1654897730 2303443265 2280478208 3403207 SRX5827019 SRS4754833 SRA886020 GEO Biology, University of Virginia 1 0.90749   0.17908   0.8017   0.5124   57   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-05-13 Larval Larval Trunk Surface Structure
52248 52248 SRR9050627 SRX5827018 SRS4754832 SRP198298 PRJNA542704 Thyroid hormone regulates distinct paths to maturation in pigment cell lineages GSE131136 Transcriptome Analysis Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.   pubmed:31140974;pubmed:33933422   Neural crest derived cells from hypothyroid post embryonic zebrafish trunks biological replicate 3 GSM3764574   tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:1073 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid Neural crest derived cells from hypothyroid post embryonic zebrafish trunks biological replicate 3 Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. sox10:Cre+ cells from post embryonic zebrafish trunk tissue Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms. cell type:1073 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid GSM3764574 GSM3764574: Neural crest derived cells from hypothyroid post embryonic zebrafish trunks biological replicate 3; Danio rerio; RNA Seq GSM3764574   1 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP198298   dangling references:treat as unmapped hypo1_possorted_genome_bam.bam 10X Genomics bam file 15530826765.0 272470645.0 GSM3764574 r1 0:57 A:4458931221;C:3243678800;G:3916155957;T:3908839406;N:3221381 57       4458931221 3243678800 3916155957 3908839406 3221381 SRX5827018 SRS4754832 SRA886020 GEO Biology, University of Virginia 1 0.94166   0.13327   0.79304   0.49472   57   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-05-13 Larval Larval Trunk Surface Structure
52249 52249 SRR9050626 SRX5827017 SRS4754831 SRP198298 PRJNA542704 Thyroid hormone regulates distinct paths to maturation in pigment cell lineages GSE131136 Transcriptome Analysis Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.   pubmed:31140974;pubmed:33933422   Neural crest derived cells from hypothyroid post embryonic zebrafish skins biological replicate 2 GSM3764573   tissue:sox10:Cre+ cells from post embryonic zebrafish skin tissue|cell type:3033 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid Neural crest derived cells from hypothyroid post embryonic zebrafish skins biological replicate 2 Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. sox10:Cre+ cells from post embryonic zebrafish skin tissue Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms. cell type:3033 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid GSM3764573 GSM3764573: Neural crest derived cells from hypothyroid post embryonic zebrafish skins biological replicate 2; Danio rerio; RNA Seq GSM3764573   1 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP198298   dangling references:treat as unmapped hypo6_possorted_genome_bam.bam 10X Genomics bam file 7642585251.0 134080443.0 GSM3764573 r1 0:57 A:2330102138;C:1530481079;G:1741129436;T:2036914417;N:3958181 57       2330102138 1530481079 1741129436 2036914417 3958181 SRX5827017 SRS4754831 SRA886020 GEO Biology, University of Virginia 1 0.92859   0.20322   0.83019   0.51386   57   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-05-13 Larval Larval Skin Surface Structure
52250 52250 SRR9050625 SRX5827016 SRS4754830 SRP198298 PRJNA542704 Thyroid hormone regulates distinct paths to maturation in pigment cell lineages GSE131136 Transcriptome Analysis Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.   pubmed:31140974;pubmed:33933422   Neural crest derived cells from hypothyroid juvenile zebrafish trunks biological replicate 1 GSM3764572   tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:2135 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 11 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid Neural crest derived cells from hypothyroid juvenile zebrafish trunks biological replicate 1 Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. sox10:Cre+ cells from post embryonic zebrafish trunk tissue Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms. cell type:2135 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 11 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid GSM3764572 GSM3764572: Neural crest derived cells from hypothyroid juvenile zebrafish trunks biological replicate 1; Danio rerio; RNA Seq GSM3764572   1 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP198298   dangling references:treat as unmapped hypo7_possorted_genome_bam.bam 10X Genomics bam file 5078170983.0 89090719.0 GSM3764572 r1 0:57 A:1526791201;C:989860604;G:1192544480;T:1366270035;N:2704663 57       1526791201 989860604 1192544480 1366270035 2704663 SRX5827016 SRS4754830 SRA886020 GEO Biology, University of Virginia 1 0.92899   0.25348   0.83571   0.48794   57   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-05-13 Multi-stage Multi-stage Trunk Surface Structure
52251 52251 SRR9050624 SRX5827015 SRS4754829 SRP198298 PRJNA542704 Thyroid hormone regulates distinct paths to maturation in pigment cell lineages GSE131136 Transcriptome Analysis Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.   pubmed:31140974;pubmed:33933422   Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 6 GSM3764571   tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:2384 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish|treatment:Euthyroid Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 6 Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. sox10:Cre+ cells from post embryonic zebrafish trunk tissue Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms. cell type:2384 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish|treatment:Euthyroid GSM3764571 GSM3764571: Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 6; Danio rerio; RNA Seq GSM3764571   1 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP198298   dangling references:treat as unmapped eu4_possorted_genome_bam.bam 10X Genomics bam file 5411416524.0 94937132.0 GSM3764571 r1 0:57 A:1638197208;C:1052881199;G:1241396499;T:1476057783;N:2883835 57       1638197208 1052881199 1241396499 1476057783 2883835 SRX5827015 SRS4754829 SRA886020 GEO Biology, University of Virginia 1 0.91678   0.23274   0.83435   0.51765   57   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-05-13 Larval Larval Trunk Surface Structure
52252 52252 SRR9050623 SRX5827014 SRS4754828 SRP198298 PRJNA542704 Thyroid hormone regulates distinct paths to maturation in pigment cell lineages GSE131136 Transcriptome Analysis Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.   pubmed:31140974;pubmed:33933422   Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 5 GSM3764570   tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:807 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish|treatment:Euthyroid Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 5 Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. sox10:Cre+ cells from post embryonic zebrafish trunk tissue Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms. cell type:807 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish|treatment:Euthyroid GSM3764570 GSM3764570: Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 5; Danio rerio; RNA Seq GSM3764570   1 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP198298   dangling references:treat as unmapped eu3_possorted_genome_bam.bam 10X Genomics bam file 8326974105.0 146087265.0 GSM3764570 r1 0:57 A:2330538697;C:1602893033;G:2265568086;T:2124697512;N:3276777 57       2330538697 1602893033 2265568086 2124697512 3276777 SRX5827014 SRS4754828 SRA886020 GEO Biology, University of Virginia 1 0.91032   0.14841   0.81207   0.52798   57   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-05-13 Larval Larval Trunk Surface Structure
52253 52253 SRR9050622 SRX5827013 SRS4754827 SRP198298 PRJNA542704 Thyroid hormone regulates distinct paths to maturation in pigment cell lineages GSE131136 Transcriptome Analysis Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.   pubmed:31140974;pubmed:33933422   Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 4 GSM3764569   tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:808 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish|treatment:Euthyroid Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 4 Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. sox10:Cre+ cells from post embryonic zebrafish trunk tissue Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms. cell type:808 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish|treatment:Euthyroid GSM3764569 GSM3764569: Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 4; Danio rerio; RNA Seq GSM3764569   1 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP198298   dangling references:treat as unmapped eu2_possorted_genome_bam.bam 10X Genomics bam file 9524985741.0 167105013.0 GSM3764569 r1 0:57 A:2659154932;C:1836434156;G:2596847773;T:2428811653;N:3737227 57       2659154932 1836434156 2596847773 2428811653 3737227 SRX5827013 SRS4754827 SRA886020 GEO Biology, University of Virginia 1 0.91042   0.14492   0.81148   0.53287   57   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-05-13 Larval Larval Trunk Surface Structure
52254 52254 SRR9050621 SRX5827012 SRS4754826 SRP198298 PRJNA542704 Thyroid hormone regulates distinct paths to maturation in pigment cell lineages GSE131136 Transcriptome Analysis Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.   pubmed:31140974;pubmed:33933422   Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 3 GSM3764568   tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:944 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish|treatment:Euthyroid Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 3 Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. sox10:Cre+ cells from post embryonic zebrafish trunk tissue Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms. cell type:944 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish|treatment:Euthyroid GSM3764568 GSM3764568: Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 3; Danio rerio; RNA Seq GSM3764568   1 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP198298   dangling references:treat as unmapped eu1_possorted_genome_bam.bam 10X Genomics bam file 14548569306.0 255238058.0 GSM3764568 r1 0:57 A:4144426475;C:3024945467;G:3685756189;T:3690427238;N:3013937 57       4144426475 3024945467 3685756189 3690427238 3013937 SRX5827012 SRS4754826 SRA886020 GEO Biology, University of Virginia 1 0.94033   0.12393   0.79338   0.50069   57   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-05-13 Larval Larval Trunk Surface Structure
52255 52255 SRR9050620 SRX5827011 SRS4754825 SRP198298 PRJNA542704 Thyroid hormone regulates distinct paths to maturation in pigment cell lineages GSE131136 Transcriptome Analysis Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.   pubmed:31140974;pubmed:33933422   Neural crest derived cells from euthyroid post embryonic zebrafish skins biological replicate 2 GSM3764567   tissue:sox10:Cre+ cells from post embryonic zebrafish skin tissue|cell type:3008 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from skins. Zebrafish range in stage from 7.2 10.4 SSL.|treatment:Euthyroid Neural crest derived cells from euthyroid post embryonic zebrafish skins biological replicate 2 Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. sox10:Cre+ cells from post embryonic zebrafish skin tissue Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms. cell type:3008 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from skins. Zebrafish range in stage from 7.2 10.4 SSL.|treatment:Euthyroid GSM3764567 GSM3764567: Neural crest derived cells from euthyroid post embryonic zebrafish skins biological replicate 2; Danio rerio; RNA Seq GSM3764567   1 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP198298   dangling references:treat as unmapped eu5_possorted_genome_bam.bam 10X Genomics bam file 7562050749.0 132667557.0 GSM3764567 r1 0:57 A:2291130941;C:1508834109;G:1752506997;T:2005478206;N:4100496 57       2291130941 1508834109 1752506997 2005478206 4100496 SRX5827011 SRS4754825 SRA886020 GEO Biology, University of Virginia 1 0.92351   0.19606   0.82913   0.5204   57   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-05-13 Larval Larval Skin Surface Structure
52256 52256 SRR9050619 SRX5827010 SRS4754824 SRP198298 PRJNA542704 Thyroid hormone regulates distinct paths to maturation in pigment cell lineages GSE131136 Transcriptome Analysis Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.   pubmed:31140974;pubmed:33933422   Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 1 GSM3764566   tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:2168 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Zebrafish were stage 11 SSL stage juvenile.|treatment:Euthyroid Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 1 Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. sox10:Cre+ cells from post embryonic zebrafish trunk tissue Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms. cell type:2168 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Zebrafish were stage 11 SSL stage juvenile.|treatment:Euthyroid GSM3764566 GSM3764566: Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 1; Danio rerio; RNA Seq GSM3764566   1 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP198298   dangling references:treat as unmapped eu6_possorted_genome_bam.bam 10X Genomics bam file 5005233954.0 87811122.0 GSM3764566 r1 0:57 A:1531421605;C:966957285;G:1151579626;T:1352667292;N:2608146 57       1531421605 966957285 1151579626 1352667292 2608146 SRX5827010 SRS4754824 SRA886020 GEO Biology, University of Virginia 1 0.92288   0.25231   0.83479   0.5014   57   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-05-13 Multi-stage Multi-stage Trunk Surface Structure
55221 55221 SRR10182211 SRX6902836 SRS5434733 SRP223244 PRJNA574059 Cellular diversity of the regenerating caudal fin GSE137971 Transcriptome Analysis single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies filtered through 40 µm cell strainers and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging alignment to zebrafish reference genome GRCz10 and feature counting based on Ensembl release 91 cellranger count.   pubmed:32851162   1dpa fin1 scRNA GSM4095395   source name:1dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:1 day post amputation 1dpa fin1 scRNA All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell. 1dpa caudal fin   We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility with system water temperature at 28.5˚C and a day night cycle controlled as 14 hr light/10 hr dark. strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:1 day post amputation GSM4095395 GSM4095395: 1dpa fin1 scRNA; Danio rerio; RNA Seq GSM4095395   1 We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics GEO Accession:GSM4095395 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP223244     1dpa1_S1_L002_R1_001.fastq.gz 1dpa1_S1_L002_R2_001.fastq.gz fastq fastq 3515690517.0 34808817.0 GSM4095395 r1 0:26 1:75 A:1021208515;C:750623954;G:773148636;T:968849435;N:1859977 26 75     1021208515 750623954 773148636 968849435 1859977 SRX6902836 SRS5434733 SRA968154 GEO Ting Wang, Genetics, Washington University St Louis 2 0.00195 0.91495 0.00089 0.10966 0.99699 0.84855 0.35643 0.59738 26 75 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-09-25 Adult Adult Fin Surface Structure
55222 55222 SRR10182210 SRX6902835 SRS5434732 SRP223244 PRJNA574059 Cellular diversity of the regenerating caudal fin GSE137971 Transcriptome Analysis single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies filtered through 40 µm cell strainers and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging alignment to zebrafish reference genome GRCz10 and feature counting based on Ensembl release 91 cellranger count.   pubmed:32851162   preinjury fin2 scRNA GSM4095394   source name:Preinjury caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury preinjury fin2 scRNA All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell. Preinjury caudal fin   We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility with system water temperature at 28.5˚C and a day night cycle controlled as 14 hr light/10 hr dark. strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury GSM4095394 GSM4095394: preinjury fin2 scRNA; Danio rerio; RNA Seq GSM4095394   1 We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics GEO Accession:GSM4095394 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP223244     samp2_S2_L002_R2_001.fastq.gz samp2_S2_L002_R1_001.fastq.gz fastq fastq 14313306001.0 141715901.0 GSM4095394 r1 0:26 1:75 A:4080921082;C:3121900376;G:3341495424;T:3761528384;N:7460735 26 75     4080921082 3121900376 3341495424 3761528384 7460735 SRX6902835 SRS5434732 SRA968154 GEO Ting Wang, Genetics, Washington University St Louis 2 0.0029 0.89943 0.00115 0.07948 0.99543 0.8714 0.29607 0.47916 26 75 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-09-25 Adult Adult Fin Surface Structure
55223 55223 SRR10182209 SRX6902834 SRS5434731 SRP223244 PRJNA574059 Cellular diversity of the regenerating caudal fin GSE137971 Transcriptome Analysis single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies filtered through 40 µm cell strainers and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging alignment to zebrafish reference genome GRCz10 and feature counting based on Ensembl release 91 cellranger count.   pubmed:32851162   preinjury fin1 scRNA GSM4095393   source name:Preinjury caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury preinjury fin1 scRNA All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell. Preinjury caudal fin   We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility with system water temperature at 28.5˚C and a day night cycle controlled as 14 hr light/10 hr dark. strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury GSM4095393 GSM4095393: preinjury fin1 scRNA; Danio rerio; RNA Seq GSM4095393   1 We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics GEO Accession:GSM4095393 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP223244     samp1_S1_L001_R1_001.fastq.gz samp1_S1_L001_R2_001.fastq.gz fastq fastq 14610147425.0 144654925.0 GSM4095393 r1 0:26 1:75 A:4066051353;C:3189039694;G:3388950081;T:3856651906;N:109454391 26 75     4066051353 3189039694 3388950081 3856651906 109454391 SRX6902834 SRS5434731 SRA968154 GEO Ting Wang, Genetics, Washington University St Louis 2 0.0024 0.87757 0.00072 0.08379 0.99504 0.85269 0.34276 0.52515 26 75 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-09-25 Adult Adult Fin Surface Structure
55224 55224 SRR10182216 SRX6902833 SRS5434730 SRP223244 PRJNA574059 Cellular diversity of the regenerating caudal fin GSE137971 Transcriptome Analysis single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies filtered through 40 µm cell strainers and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging alignment to zebrafish reference genome GRCz10 and feature counting based on Ensembl release 91 cellranger count.   pubmed:32851162   4dpa fin2 scRNA GSM4095400   source name:4dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:4 day post amputation 4dpa fin2 scRNA All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell. 4dpa caudal fin   We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility with system water temperature at 28.5˚C and a day night cycle controlled as 14 hr light/10 hr dark. strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:4 day post amputation GSM4095400 GSM4095400: 4dpa fin2 scRNA; Danio rerio; RNA Seq GSM4095400   1 We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics GEO Accession:GSM4095400 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP223244     4dpa2_S2_L002_R1_001.fastq.gz 4dpa2_S2_L002_R2_001.fastq.gz fastq fastq 12205232082.0 120843882.0 GSM4095400 r1 0:26 1:75 A:3462691218;C:2662402586;G:2782962664;T:3293833482;N:3342132 26 75     3462691218 2662402586 2782962664 3293833482 3342132 SRX6902833 SRS5434730 SRA968154 GEO Ting Wang, Genetics, Washington University St Louis 2 0.00216 0.90418 0.00058 0.09381 0.99488 0.82666 0.33993 0.51619 26 75 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-09-25 Adult Adult Fin Surface Structure
55225 55225 SRR10182215 SRX6902832 SRS5434729 SRP223244 PRJNA574059 Cellular diversity of the regenerating caudal fin GSE137971 Transcriptome Analysis single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies filtered through 40 µm cell strainers and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging alignment to zebrafish reference genome GRCz10 and feature counting based on Ensembl release 91 cellranger count.   pubmed:32851162   4dpa fin1 scRNA GSM4095399   source name:4dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:4 day post amputation 4dpa fin1 scRNA All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell. 4dpa caudal fin   We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility with system water temperature at 28.5˚C and a day night cycle controlled as 14 hr light/10 hr dark. strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:4 day post amputation GSM4095399 GSM4095399: 4dpa fin1 scRNA; Danio rerio; RNA Seq GSM4095399   1 We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics GEO Accession:GSM4095399 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP223244     4dpa1_S1_L001_R1_001.fastq.gz 4dpa1_S1_L001_R2_001.fastq.gz fastq fastq 14335848494.0 141939094.0 GSM4095399 r1 0:26 1:75 A:4028586492;C:3145713740;G:3334469278;T:3823390760;N:3688224 26 75     4028586492 3145713740 3334469278 3823390760 3688224 SRX6902832 SRS5434729 SRA968154 GEO Ting Wang, Genetics, Washington University St Louis 2 0.00214 0.90496 0.00068 0.10148 0.99494 0.82014 0.36363 0.54339 26 75 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-09-25 Adult Adult Fin Surface Structure
55226 55226 SRR10182214 SRX6902831 SRS5434728 SRP223244 PRJNA574059 Cellular diversity of the regenerating caudal fin GSE137971 Transcriptome Analysis single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies filtered through 40 µm cell strainers and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging alignment to zebrafish reference genome GRCz10 and feature counting based on Ensembl release 91 cellranger count.   pubmed:32851162   2dpa fin2 scRNA GSM4095398   source name:2dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:2 day post amputation 2dpa fin2 scRNA All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell. 2dpa caudal fin   We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility with system water temperature at 28.5˚C and a day night cycle controlled as 14 hr light/10 hr dark. strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:2 day post amputation GSM4095398 GSM4095398: 2dpa fin2 scRNA; Danio rerio; RNA Seq GSM4095398   1 We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics GEO Accession:GSM4095398 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP223244     2dpa2_S2_L002_R1_001.fastq.gz 2dpa2_S2_L002_R2_001.fastq.gz fastq fastq 14592805725.0 144483225.0 GSM4095398 r1 0:26 1:75 A:4087287462;C:3228369053;G:3401290297;T:3861324848;N:14534065 26 75     4087287462 3228369053 3401290297 3861324848 14534065 SRX6902831 SRS5434728 SRA968154 GEO Ting Wang, Genetics, Washington University St Louis 2 0.00231 0.91223 0.00055 0.08705 0.99452 0.82627 0.30769 0.5211 26 75 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-09-25 Adult Adult Fin Surface Structure
55227 55227 SRR10182213 SRX6902830 SRS5434727 SRP223244 PRJNA574059 Cellular diversity of the regenerating caudal fin GSE137971 Transcriptome Analysis single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies filtered through 40 µm cell strainers and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging alignment to zebrafish reference genome GRCz10 and feature counting based on Ensembl release 91 cellranger count.   pubmed:32851162   2dpa fin1 scRNA GSM4095397   source name:2dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:2 day post amputation 2dpa fin1 scRNA All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell. 2dpa caudal fin   We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility with system water temperature at 28.5˚C and a day night cycle controlled as 14 hr light/10 hr dark. strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:2 day post amputation GSM4095397 GSM4095397: 2dpa fin1 scRNA; Danio rerio; RNA Seq GSM4095397   1 We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics GEO Accession:GSM4095397 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP223244     2dpa1_S1_L001_R1_001.fastq.gz 2dpa1_S1_L001_R2_001.fastq.gz fastq fastq 15317979261.0 151663161.0 GSM4095397 r1 0:26 1:75 A:4303056842;C:3349998898;G:3533853775;T:4116083703;N:14986043 26 75     4303056842 3349998898 3533853775 4116083703 14986043 SRX6902830 SRS5434727 SRA968154 GEO Ting Wang, Genetics, Washington University St Louis 2 0.0022 0.9122 0.0006 0.09555 0.99504 0.82203 0.33222 0.52299 26 75 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-09-25 Adult Adult Fin Surface Structure
55228 55228 SRR10182212 SRX6902829 SRS5434726 SRP223244 PRJNA574059 Cellular diversity of the regenerating caudal fin GSE137971 Transcriptome Analysis single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies filtered through 40 µm cell strainers and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging alignment to zebrafish reference genome GRCz10 and feature counting based on Ensembl release 91 cellranger count.   pubmed:32851162   1dpa fin2 scRNA GSM4095396   source name:1dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:1 day post amputation 1dpa fin2 scRNA All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell. 1dpa caudal fin   We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility with system water temperature at 28.5˚C and a day night cycle controlled as 14 hr light/10 hr dark. strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:1 day post amputation GSM4095396 GSM4095396: 1dpa fin2 scRNA; Danio rerio; RNA Seq GSM4095396   1 We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics GEO Accession:GSM4095396 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP223244     1dpa2_S2_L002_R2_001.fastq.gz 1dpa2_S2_L002_R1_001.fastq.gz fastq fastq 10934230609.0 108259709.0 GSM4095396 r1 0:26 1:75 A:3111673507;C:2358969825;G:2438293271;T:3019487882;N:5806124 26 75     3111673507 2358969825 2438293271 3019487882 5806124 SRX6902829 SRS5434726 SRA968154 GEO Ting Wang, Genetics, Washington University St Louis 2 0.00198 0.92416 0.00054 0.08626 0.99596 0.83808 0.29818 0.52586 26 75 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-09-25 Adult Adult Fin Surface Structure
59887 59887 SRR12067711 SRX8595501 SRS6886082 SRP268312 PRJNA641114 Single cell transcriptomic analysis 30 hpf Zebrafish trunks GSE152982 Other Here we performed single cell RNAseq analysis of whole wildtype zebrafish trunks at 30hpf using 10x Genomics' Chromium platform. 22 distinct cell populations were identified spanning all three embryonic germ layers. Overall design: Whole trunks excised from 30 embryos at 30 hpf were dissociated using a cold protease dissociation protocol. Barcoding of cells and and cDNA library construction was carried out using 10X Genomics' Chromium platform.   pubmed:34234366   Zf 30h trunk GSM4631066   source name:Zebrafish Trunks|age:30 hpf|tissue:trunk|genotype:wildtype Zf 30h trunk All processing was performed in 10X Genomics CellRanger v3.0.2 using default parameters Raw basecall files were assembled into fastq files using 'mkfastq' function The 'count' function was used to align Fastq files to zebrafish genome v.11 and to obtain the gene expression matrices Genome build: GRCz11 Supplementary files format and content: mtx matrix files Zebrafish Trunks   Whole wildtype zebrafish trunks at 30 hpf were dissociated into a single cell suspension using a cold protease treatment.Single cell suspensions were processed through the Chromium platform 10X Genomics to generate single cell cDNA libraries cDNA was amplified by PCR and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol   age:30 hpf|tissue:trunk|genotype:wildtype GSM4631066 GSM4631066: Zf 30h trunk; Danio rerio; RNA Seq GSM4631066   1 Whole wildtype zebrafish trunks at 30 hpf were dissociated into a single cell suspension using a cold protease treatment.Single cell suspensions were processed through the Chromium platform 10X Genomics to generate single cell cDNA libraries cDNA was amplified by PCR and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol GEO Accession:GSM4631066 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP268312   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Zf30hTrunk S1 L001 I1 001.fastq.gz read2PairFiles=Zf30hTrunk S1 L001 R1 001.fastq.gz read3PairFiles=Zf30hTrunk S1 L001 R2 001.fastq.gz Zf30hTrunk_S1_L001_I1_001.fastq.gz Zf30hTrunk_S1_L001_R1_001.fastq.gz Zf30hTrunk_S1_L001_R2_001.fastq.gz fastq fastq fastq 30568523622.0 167958921.0 GSM4631066 r1 0:8 1:27 2:147 A:8739694698;C:6736998816;G:6903125001;T:8168427703;N:20277404 8 27 147   8739694698 6736998816 6903125001 8168427703 20277404 SRX8595501 SRS6886082 SRA1089692 GEO University of South Florida 1 0.88066   0.09296   0.8506   0.50586   147   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified nextera sc single_cell_droplet 10x   United States 2020-06-22 Pharyngula Embryo Trunk Surface Structure
59888 59888 SRR12067712 SRX8595501 SRS6886082 SRP268312 PRJNA641114 Single cell transcriptomic analysis 30 hpf Zebrafish trunks GSE152982 Other Here we performed single cell RNAseq analysis of whole wildtype zebrafish trunks at 30hpf using 10x Genomics' Chromium platform. 22 distinct cell populations were identified spanning all three embryonic germ layers. Overall design: Whole trunks excised from 30 embryos at 30 hpf were dissociated using a cold protease dissociation protocol. Barcoding of cells and and cDNA library construction was carried out using 10X Genomics' Chromium platform.   pubmed:34234366   Zf 30h trunk GSM4631066   source name:Zebrafish Trunks|age:30 hpf|tissue:trunk|genotype:wildtype Zf 30h trunk All processing was performed in 10X Genomics CellRanger v3.0.2 using default parameters Raw basecall files were assembled into fastq files using 'mkfastq' function The 'count' function was used to align Fastq files to zebrafish genome v.11 and to obtain the gene expression matrices Genome build: GRCz11 Supplementary files format and content: mtx matrix files Zebrafish Trunks   Whole wildtype zebrafish trunks at 30 hpf were dissociated into a single cell suspension using a cold protease treatment.Single cell suspensions were processed through the Chromium platform 10X Genomics to generate single cell cDNA libraries cDNA was amplified by PCR and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol   age:30 hpf|tissue:trunk|genotype:wildtype GSM4631066 GSM4631066: Zf 30h trunk; Danio rerio; RNA Seq GSM4631066   1 Whole wildtype zebrafish trunks at 30 hpf were dissociated into a single cell suspension using a cold protease treatment.Single cell suspensions were processed through the Chromium platform 10X Genomics to generate single cell cDNA libraries cDNA was amplified by PCR and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol GEO Accession:GSM4631066 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP268312   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Zf30hTrunk S1 L002 I1 001.fastq.gz read2PairFiles=Zf30hTrunk S1 L002 R1 001.fastq.gz read3PairFiles=Zf30hTrunk S1 L002 R2 001.fastq.gz Zf30hTrunk_S1_L002_I1_001.fastq.gz Zf30hTrunk_S1_L002_R1_001.fastq.gz Zf30hTrunk_S1_L002_R2_001.fastq.gz fastq fastq fastq 31428372976.0 172683368.0 GSM4631066 r2 0:8 1:27 2:147 A:8978925123;C:6926043302;G:7091713953;T:8399543364;N:32147234 8 27 147   8978925123 6926043302 7091713953 8399543364 32147234 SRX8595501 SRS6886082 SRA1089692 GEO University of South Florida 1 0.87666   0.09235   0.85277   0.49776   147   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified nextera sc single_cell_droplet 10x   United States 2020-06-22 Pharyngula Embryo Trunk Surface Structure
61429 61429 SRR12749699 SRX9221655 SRS7455356 SRP285950 PRJNA666695 Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae GSE158851 Transcriptome Analysis Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation. Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform and sequenced using Illumina NovaSeq 6000. Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets previously described by our group to govern zebrafish fin regeneration and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.   pubmed:34732706;pubmed:35664055   Uncut caudal fin scRNA GSM4812244   source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation Uncut caudal fin scRNA Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format : the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination ; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'. caudal fin   Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222 Sigma in zebrafish water. Approximately 150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer’s instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.   tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation GSM4812244 GSM4812244: Uncut caudal fin scRNA; Danio rerio; RNA Seq GSM4812244   1 Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222 Sigma in zebrafish water. Approximately 150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument. GEO Accession:GSM4812244 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP285950   loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=Uncut S8 L001 R1 001.fastq.gz read2PairFiles=Uncut S8 L001 R2 001.fastq.gz read3PairFiles=Uncut S8 L001 I1 001.fastq.gz Uncut_S8_L001_I1_001.fastq.gz Uncut_S8_L001_R1_001.fastq.gz Uncut_S8_L001_R2_001.fastq.gz fastq fastq fastq 18909629967.0 153736829.0 GSM4812244 r1 0:28 1:87 2:8 A:5220924848;C:4279280050;G:4788532540;T:4619612909;N:1279620 28 87 8   5220924848 4279280050 4788532540 4619612909 1279620 SRX9221655 SRS7455356 SRA1136463 GEO Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm 1 0.63376   0.11724   0.8393   0.55679   87   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   France 2020-09-30 Larval Larval Fin Surface Structure
61430 61430 SRR12749700 SRX9221655 SRS7455356 SRP285950 PRJNA666695 Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae GSE158851 Transcriptome Analysis Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation. Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform and sequenced using Illumina NovaSeq 6000. Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets previously described by our group to govern zebrafish fin regeneration and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.   pubmed:34732706;pubmed:35664055   Uncut caudal fin scRNA GSM4812244   source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation Uncut caudal fin scRNA Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format : the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination ; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'. caudal fin   Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222 Sigma in zebrafish water. Approximately 150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer’s instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.   tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation GSM4812244 GSM4812244: Uncut caudal fin scRNA; Danio rerio; RNA Seq GSM4812244   1 Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222 Sigma in zebrafish water. Approximately 150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument. GEO Accession:GSM4812244 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP285950   loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=Uncut S8 L002 R1 001.fastq.gz read2PairFiles=Uncut S8 L002 R2 001.fastq.gz read3PairFiles=Uncut S8 L002 I1 001.fastq.gz Uncut_S8_L002_I1_001.fastq.gz Uncut_S8_L002_R1_001.fastq.gz Uncut_S8_L002_R2_001.fastq.gz fastq fastq fastq 18967585107.0 154208009.0 GSM4812244 r2 0:28 1:87 2:8 A:5236542259;C:4292274179;G:4804216460;T:4633355352;N:1196857 28 87 8   5236542259 4292274179 4804216460 4633355352 1196857 SRX9221655 SRS7455356 SRA1136463 GEO Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm 1 0.63437   0.11726   0.83857   0.5661   87   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   France 2020-09-30 Larval Larval Fin Surface Structure
61431 61431 SRR12749697 SRX9221654 SRS7455355 SRP285950 PRJNA666695 Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae GSE158851 Transcriptome Analysis Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation. Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform and sequenced using Illumina NovaSeq 6000. Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets previously described by our group to govern zebrafish fin regeneration and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.   pubmed:34732706;pubmed:35664055   Cut caudal fin scRNA GSM4812243   source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours Cut caudal fin scRNA Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format : the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination ; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'. caudal fin   Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222 Sigma in zebrafish water. Approximately 150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer’s instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.   tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours GSM4812243 GSM4812243: Cut caudal fin scRNA; Danio rerio; RNA Seq GSM4812243   1 Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222 Sigma in zebrafish water. Approximately 150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument. GEO Accession:GSM4812243 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP285950   loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=Cut S7 L001 R1 001.fastq.gz read2PairFiles=Cut S7 L001 R2 001.fastq.gz read3PairFiles=Cut S7 L001 I1 001.fastq.gz Cut_S7_L001_I1_001.fastq.gz Cut_S7_L001_R1_001.fastq.gz Cut_S7_L001_R2_001.fastq.gz fastq fastq fastq 17453571711.0 141898957.0 GSM4812243 r1 0:28 1:87 2:8 A:4820960991;C:3908308491;G:4347557585;T:4375565175;N:1179469 28 87 8   4820960991 3908308491 4347557585 4375565175 1179469 SRX9221654 SRS7455355 SRA1136463 GEO Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm 1 0.63902   0.11232   0.82235   0.50797   87   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   France 2020-09-30 Larval Larval Fin Surface Structure
61432 61432 SRR12749698 SRX9221654 SRS7455355 SRP285950 PRJNA666695 Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae GSE158851 Transcriptome Analysis Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation. Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform and sequenced using Illumina NovaSeq 6000. Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets previously described by our group to govern zebrafish fin regeneration and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.   pubmed:34732706;pubmed:35664055   Cut caudal fin scRNA GSM4812243   source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours Cut caudal fin scRNA Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format : the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination ; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'. caudal fin   Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222 Sigma in zebrafish water. Approximately 150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer’s instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.   tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours GSM4812243 GSM4812243: Cut caudal fin scRNA; Danio rerio; RNA Seq GSM4812243   1 Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222 Sigma in zebrafish water. Approximately 150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument. GEO Accession:GSM4812243 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP285950   loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=Cut S7 L002 R1 001.fastq.gz read2PairFiles=Cut S7 L002 R2 001.fastq.gz read3PairFiles=Cut S7 L002 I1 001.fastq.gz Cut_S7_L002_I1_001.fastq.gz Cut_S7_L002_R1_001.fastq.gz Cut_S7_L002_R2_001.fastq.gz fastq fastq fastq 17511283926.0 142368162.0 GSM4812243 r2 0:28 1:87 2:8 A:4836849959;C:3920920286;G:4362769830;T:4389644044;N:1099807 28 87 8   4836849959 3920920286 4362769830 4389644044 1099807 SRX9221654 SRS7455355 SRA1136463 GEO Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm 1 0.63847   0.11249   0.82231   0.51524   87   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   France 2020-09-30 Larval Larval Fin Surface Structure
65124 65124 SRR14935604 SRX11248236 SRS9294118 SRP325962 PRJNA742206 Heterogeneity and molecular programming of progenitors for motor neurons and oligodendrocytes GSE179096 Other The pMN domain is a restricted domain in the ventral spinal cords defined by the expression of olig2 gene. The fate determination of pMN progenitors is highly temporally and spatially regulated with motor neurons and oligodendrocyte progenitor cells OPCs developing sequentially. Insight into the heterogeneity and molecular programs of pMN progenitors is currently lacking. With the zebrafish model we identified multiple states of neural progenitors using single cell sequencing: proliferating progenitors common progenitors for both motor neurons and OPCs and restricted precursors for either motor neurons or OPCs. We found specific molecular programs for neural progenitor fate transition and manipulations of representative genes in the motor neuron or OPC lineage confirmed their critical role in cell fate determination. Deciphering progenitor heterogeneity and molecular mechanisms for these transitions will elucidate the formation of complex neuron glia networks in the central nervous system during development and understand the basis of neurodevelopmental disorders. Overall design: olig2+ cells were isolated from the trunks of Tgolig2:dsred by FACS and underwent scRNA seq   pubmed:36063998   olig2+ cells in zebrafish trunks GSM5406686   source name:Tgolig2:dsred trunks|developmental stage:42 hpf|genotype:Tg olig2:dsred|tissue:trunk|cell type:fluorescent cells from Tgolig2:dsred trunks olig2+ cells in zebrafish trunks Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Genes detectable in more than two cells were defined as “expressed”. Cells with <1000 genes detected were removed. Counts were normalized to 10000 and transformed into logarithmic scales. A neighborhood graph was embedded using UMAP displaying the top 4000 highly variable genes across cells. Cells were clustered by the Louvain Algorithm. The trajectory interface of all cell clusters was done using the layout 'fa'. These analyses were performed by the Python based SCANPY package Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Tgolig2:dsred trunks   Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell 3’ Library and Gel Bead kit V3   developmental stage:42 hpf|genotype:Tg olig2:dsred|tissue:trunk|cell type:fluorescent cells from Tgolig2:dsred trunks GSM5406686 GSM5406686: olig2+ cells in zebrafish trunks; Danio rerio; RNA Seq GSM5406686   1 Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell three prime Library and Gel Bead kit V3 GEO Accession:GSM5406686 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP325962     191269A_Z_Olig2_1_1_R1.fq.gz 191269A_Z_Olig2_1_1_R2.fq.gz fastq fastq 31400412000.0 104668040.0 GSM5406686 r1 0:150 1:150 A:6848745621;C:5731974961;G:10959380121;T:7859959179;N:352118 150 150     6848745621 5731974961 10959380121 7859959179 352118 SRX11248236 SRS9294118 SRA1251944 GEO Nantong University 2 0.0 0.89636 0.0 0.20375 1.0 0.78575   0.50155 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2021-06-29 Pharyngula Embryo Trunk Surface Structure
65125 65125 SRR14935605 SRX11248236 SRS9294118 SRP325962 PRJNA742206 Heterogeneity and molecular programming of progenitors for motor neurons and oligodendrocytes GSE179096 Other The pMN domain is a restricted domain in the ventral spinal cords defined by the expression of olig2 gene. The fate determination of pMN progenitors is highly temporally and spatially regulated with motor neurons and oligodendrocyte progenitor cells OPCs developing sequentially. Insight into the heterogeneity and molecular programs of pMN progenitors is currently lacking. With the zebrafish model we identified multiple states of neural progenitors using single cell sequencing: proliferating progenitors common progenitors for both motor neurons and OPCs and restricted precursors for either motor neurons or OPCs. We found specific molecular programs for neural progenitor fate transition and manipulations of representative genes in the motor neuron or OPC lineage confirmed their critical role in cell fate determination. Deciphering progenitor heterogeneity and molecular mechanisms for these transitions will elucidate the formation of complex neuron glia networks in the central nervous system during development and understand the basis of neurodevelopmental disorders. Overall design: olig2+ cells were isolated from the trunks of Tgolig2:dsred by FACS and underwent scRNA seq   pubmed:36063998   olig2+ cells in zebrafish trunks GSM5406686   source name:Tgolig2:dsred trunks|developmental stage:42 hpf|genotype:Tg olig2:dsred|tissue:trunk|cell type:fluorescent cells from Tgolig2:dsred trunks olig2+ cells in zebrafish trunks Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Genes detectable in more than two cells were defined as “expressed”. Cells with <1000 genes detected were removed. Counts were normalized to 10000 and transformed into logarithmic scales. A neighborhood graph was embedded using UMAP displaying the top 4000 highly variable genes across cells. Cells were clustered by the Louvain Algorithm. The trajectory interface of all cell clusters was done using the layout 'fa'. These analyses were performed by the Python based SCANPY package Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Tgolig2:dsred trunks   Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell 3’ Library and Gel Bead kit V3   developmental stage:42 hpf|genotype:Tg olig2:dsred|tissue:trunk|cell type:fluorescent cells from Tgolig2:dsred trunks GSM5406686 GSM5406686: olig2+ cells in zebrafish trunks; Danio rerio; RNA Seq GSM5406686   1 Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell three prime Library and Gel Bead kit V3 GEO Accession:GSM5406686 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP325962     191269A_Z_Olig2_2_1_R1.fq.gz 191269A_Z_Olig2_2_1_R2.fq.gz fastq fastq 24958600500.0 83195335.0 GSM5406686 r2 0:150 1:150 A:5431710090;C:4568888734;G:8717963207;T:6239757593;N:280876 150 150     5431710090 4568888734 8717963207 6239757593 280876 SRX11248236 SRS9294118 SRA1251944 GEO Nantong University 2 0.0 0.89635 0.0 0.20299 1.0 0.78453   0.50241 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2021-06-29 Pharyngula Embryo Trunk Surface Structure
65126 65126 SRR14935606 SRX11248236 SRS9294118 SRP325962 PRJNA742206 Heterogeneity and molecular programming of progenitors for motor neurons and oligodendrocytes GSE179096 Other The pMN domain is a restricted domain in the ventral spinal cords defined by the expression of olig2 gene. The fate determination of pMN progenitors is highly temporally and spatially regulated with motor neurons and oligodendrocyte progenitor cells OPCs developing sequentially. Insight into the heterogeneity and molecular programs of pMN progenitors is currently lacking. With the zebrafish model we identified multiple states of neural progenitors using single cell sequencing: proliferating progenitors common progenitors for both motor neurons and OPCs and restricted precursors for either motor neurons or OPCs. We found specific molecular programs for neural progenitor fate transition and manipulations of representative genes in the motor neuron or OPC lineage confirmed their critical role in cell fate determination. Deciphering progenitor heterogeneity and molecular mechanisms for these transitions will elucidate the formation of complex neuron glia networks in the central nervous system during development and understand the basis of neurodevelopmental disorders. Overall design: olig2+ cells were isolated from the trunks of Tgolig2:dsred by FACS and underwent scRNA seq   pubmed:36063998   olig2+ cells in zebrafish trunks GSM5406686   source name:Tgolig2:dsred trunks|developmental stage:42 hpf|genotype:Tg olig2:dsred|tissue:trunk|cell type:fluorescent cells from Tgolig2:dsred trunks olig2+ cells in zebrafish trunks Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Genes detectable in more than two cells were defined as “expressed”. Cells with <1000 genes detected were removed. Counts were normalized to 10000 and transformed into logarithmic scales. A neighborhood graph was embedded using UMAP displaying the top 4000 highly variable genes across cells. Cells were clustered by the Louvain Algorithm. The trajectory interface of all cell clusters was done using the layout 'fa'. These analyses were performed by the Python based SCANPY package Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Tgolig2:dsred trunks   Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell 3’ Library and Gel Bead kit V3   developmental stage:42 hpf|genotype:Tg olig2:dsred|tissue:trunk|cell type:fluorescent cells from Tgolig2:dsred trunks GSM5406686 GSM5406686: olig2+ cells in zebrafish trunks; Danio rerio; RNA Seq GSM5406686   1 Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell three prime Library and Gel Bead kit V3 GEO Accession:GSM5406686 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP325962     191269A_Z_Olig2_3_1_R1.fq.gz 191269A_Z_Olig2_3_1_R2.fq.gz fastq fastq 20693368500.0 68977895.0 GSM5406686 r3 0:150 1:150 A:4513259900;C:3774781009;G:7221748955;T:5183345869;N:232767 150 150     4513259900 3774781009 7221748955 5183345869 232767 SRX11248236 SRS9294118 SRA1251944 GEO Nantong University 2 0.0 0.89637 0.0 0.20432 1.0 0.78439   0.4973 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2021-06-29 Pharyngula Embryo Trunk Surface Structure
65127 65127 SRR14935607 SRX11248236 SRS9294118 SRP325962 PRJNA742206 Heterogeneity and molecular programming of progenitors for motor neurons and oligodendrocytes GSE179096 Other The pMN domain is a restricted domain in the ventral spinal cords defined by the expression of olig2 gene. The fate determination of pMN progenitors is highly temporally and spatially regulated with motor neurons and oligodendrocyte progenitor cells OPCs developing sequentially. Insight into the heterogeneity and molecular programs of pMN progenitors is currently lacking. With the zebrafish model we identified multiple states of neural progenitors using single cell sequencing: proliferating progenitors common progenitors for both motor neurons and OPCs and restricted precursors for either motor neurons or OPCs. We found specific molecular programs for neural progenitor fate transition and manipulations of representative genes in the motor neuron or OPC lineage confirmed their critical role in cell fate determination. Deciphering progenitor heterogeneity and molecular mechanisms for these transitions will elucidate the formation of complex neuron glia networks in the central nervous system during development and understand the basis of neurodevelopmental disorders. Overall design: olig2+ cells were isolated from the trunks of Tgolig2:dsred by FACS and underwent scRNA seq   pubmed:36063998   olig2+ cells in zebrafish trunks GSM5406686   source name:Tgolig2:dsred trunks|developmental stage:42 hpf|genotype:Tg olig2:dsred|tissue:trunk|cell type:fluorescent cells from Tgolig2:dsred trunks olig2+ cells in zebrafish trunks Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Genes detectable in more than two cells were defined as “expressed”. Cells with <1000 genes detected were removed. Counts were normalized to 10000 and transformed into logarithmic scales. A neighborhood graph was embedded using UMAP displaying the top 4000 highly variable genes across cells. Cells were clustered by the Louvain Algorithm. The trajectory interface of all cell clusters was done using the layout 'fa'. These analyses were performed by the Python based SCANPY package Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Tgolig2:dsred trunks   Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell 3’ Library and Gel Bead kit V3   developmental stage:42 hpf|genotype:Tg olig2:dsred|tissue:trunk|cell type:fluorescent cells from Tgolig2:dsred trunks GSM5406686 GSM5406686: olig2+ cells in zebrafish trunks; Danio rerio; RNA Seq GSM5406686   1 Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell three prime Library and Gel Bead kit V3 GEO Accession:GSM5406686 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP325962     191269A_Z_Olig2_4_1_R1.fq.gz 191269A_Z_Olig2_4_1_R2.fq.gz fastq fastq 22347557700.0 74491859.0 GSM5406686 r4 0:150 1:150 A:4874539429;C:4084280591;G:7793747016;T:5594741104;N:249560 150 150     4874539429 4084280591 7793747016 5594741104 249560 SRX11248236 SRS9294118 SRA1251944 GEO Nantong University 2 0.0 0.89737 0.0 0.20476 1.0 0.78675   0.5017 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2021-06-29 Pharyngula Embryo Trunk Surface Structure
65589 65589 SRR15390211 SRX11692441 SRS9724035 SRP331755 PRJNA753151 scRNA seq of fin and body zebrafish melanocytes GSE181748 Transcriptome Analysis Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body whereas the acral subtype arises on the palms of the hands soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes compared to body melanocytes revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma which was generated by injecting Casper fish with MniCoopR GFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total GFP+ body cells GFP body cells GFP+ fin cells GFP fin cells. Data was then analyzed and pooled together …   pubmed:35355015   XFN GSM5510267   source name:Zebrafish fins|model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP XFN Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao Hao et al. 2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija 2019. Principal component analysis Joliffe 1986 and UMAP dimensionality reduction McInnes 2018 were performed using default parameters with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al. 2020; Hunter Moncada et al. 2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output Zebrafish fins   Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics   model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP GSM5510267 GSM5510267: XFN; Danio rerio; RNA Seq GSM5510267   1 Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics GEO Accession:GSM5510267 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP331755     2385_XFN_IGO_11718_4_S4_L001_R1_001.fastq.gz 2385_XFN_IGO_11718_4_S4_L001_R2_001.fastq.gz fastq fastq 20452607604.0 174808612.0 GSM5510267 r1 0:29 1:88 A:5729911089;C:4526353776;G:4631244451;T:5564405432;N:692856 29 88     5729911089 4526353776 4631244451 5564405432 692856 SRX11692441 SRS9724035 SRA1274997 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.00608 0.85139 0.00196 0.14282 0.99093 0.78543 0.42676 0.53168 29 88 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-09 Undetermined Adult Fin Surface Structure
65590 65590 SRR15390212 SRX11692441 SRS9724035 SRP331755 PRJNA753151 scRNA seq of fin and body zebrafish melanocytes GSE181748 Transcriptome Analysis Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body whereas the acral subtype arises on the palms of the hands soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes compared to body melanocytes revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma which was generated by injecting Casper fish with MniCoopR GFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total GFP+ body cells GFP body cells GFP+ fin cells GFP fin cells. Data was then analyzed and pooled together …   pubmed:35355015   XFN GSM5510267   source name:Zebrafish fins|model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP XFN Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao Hao et al. 2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija 2019. Principal component analysis Joliffe 1986 and UMAP dimensionality reduction McInnes 2018 were performed using default parameters with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al. 2020; Hunter Moncada et al. 2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output Zebrafish fins   Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics   model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP GSM5510267 GSM5510267: XFN; Danio rerio; RNA Seq GSM5510267   1 Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics GEO Accession:GSM5510267 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP331755     2385_XFN_IGO_11718_4_S4_L002_R1_001.fastq.gz 2385_XFN_IGO_11718_4_S4_L002_R2_001.fastq.gz fastq fastq 20056571028.0 171423684.0 GSM5510267 r2 0:29 1:88 A:5624358913;C:4435209829;G:4536840173;T:5459497012;N:665101 29 88     5624358913 4435209829 4536840173 5459497012 665101 SRX11692441 SRS9724035 SRA1274997 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.00636 0.85263 0.00229 0.14314 0.99113 0.78206 0.42564 0.53095 29 88 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-09 Undetermined Adult Fin Surface Structure
65591 65591 SRR15390209 SRX11692439 SRS9724039 SRP331755 PRJNA753151 scRNA seq of fin and body zebrafish melanocytes GSE181748 Transcriptome Analysis Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body whereas the acral subtype arises on the palms of the hands soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes compared to body melanocytes revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma which was generated by injecting Casper fish with MniCoopR GFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total GFP+ body cells GFP body cells GFP+ fin cells GFP fin cells. Data was then analyzed and pooled together …   pubmed:35355015   XFG GSM5510266   source name:Zebrafish fins|model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP+ XFG Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao Hao et al. 2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija 2019. Principal component analysis Joliffe 1986 and UMAP dimensionality reduction McInnes 2018 were performed using default parameters with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al. 2020; Hunter Moncada et al. 2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output Zebrafish fins   Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics   model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP+ GSM5510266 GSM5510266: XFG; Danio rerio; RNA Seq GSM5510266   1 Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics GEO Accession:GSM5510266 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP331755     2384_XFG_IGO_11718_3_S3_L001_R1_001.fastq.gz 2384_XFG_IGO_11718_3_S3_L001_R2_001.fastq.gz fastq fastq 21239736102.0 181536206.0 GSM5510266 r1 0:29 1:88 A:6013451435;C:4631285818;G:4786546365;T:5807740759;N:711725 29 88     6013451435 4631285818 4786546365 5807740759 711725 SRX11692439 SRS9724039 SRA1274997 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.00797 0.89811 0.00258 0.14942 0.9889 0.79259 0.38209 0.54357 29 88 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-09 Undetermined Adult Fin Surface Structure
65592 65592 SRR15390210 SRX11692439 SRS9724039 SRP331755 PRJNA753151 scRNA seq of fin and body zebrafish melanocytes GSE181748 Transcriptome Analysis Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body whereas the acral subtype arises on the palms of the hands soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes compared to body melanocytes revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma which was generated by injecting Casper fish with MniCoopR GFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total GFP+ body cells GFP body cells GFP+ fin cells GFP fin cells. Data was then analyzed and pooled together …   pubmed:35355015   XFG GSM5510266   source name:Zebrafish fins|model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP+ XFG Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao Hao et al. 2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija 2019. Principal component analysis Joliffe 1986 and UMAP dimensionality reduction McInnes 2018 were performed using default parameters with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al. 2020; Hunter Moncada et al. 2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output Zebrafish fins   Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics   model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP+ GSM5510266 GSM5510266: XFG; Danio rerio; RNA Seq GSM5510266   1 Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics GEO Accession:GSM5510266 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP331755     2384_XFG_IGO_11718_3_S3_L002_R1_001.fastq.gz 2384_XFG_IGO_11718_3_S3_L002_R2_001.fastq.gz fastq fastq 20799675234.0 177775002.0 GSM5510266 r2 0:29 1:88 A:5894902894;C:4531100030;G:4681582244;T:5691398362;N:691704 29 88     5894902894 4531100030 4681582244 5691398362 691704 SRX11692439 SRS9724039 SRA1274997 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.00787 0.89764 0.00227 0.14926 0.98821 0.78928 0.40092 0.53114 29 88 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-09 Undetermined Adult Fin Surface Structure
65593 65593 SRR15390207 SRX11692437 SRS9724034 SRP331755 PRJNA753151 scRNA seq of fin and body zebrafish melanocytes GSE181748 Transcriptome Analysis Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body whereas the acral subtype arises on the palms of the hands soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes compared to body melanocytes revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma which was generated by injecting Casper fish with MniCoopR GFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total GFP+ body cells GFP body cells GFP+ fin cells GFP fin cells. Data was then analyzed and pooled together …   pubmed:35355015   XBN GSM5510265   source name:Zebrafish body skin|model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Body|cell type:GFP XBN Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao Hao et al. 2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija 2019. Principal component analysis Joliffe 1986 and UMAP dimensionality reduction McInnes 2018 were performed using default parameters with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al. 2020; Hunter Moncada et al. 2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output Zebrafish body skin   Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics   model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Body|cell type:GFP GSM5510265 GSM5510265: XBN; Danio rerio; RNA Seq GSM5510265   1 Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics GEO Accession:GSM5510265 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP331755     2387_XBN_IGO_11718_6_S6_L001_R1_001.fastq.gz 2387_XBN_IGO_11718_6_S6_L001_R2_001.fastq.gz fastq fastq 19425231072.0 166027616.0 GSM5510265 r1 0:29 1:88 A:5317276529;C:4456617510;G:4523328168;T:5127353259;N:655606 29 88     5317276529 4456617510 4523328168 5127353259 655606 SRX11692437 SRS9724034 SRA1274997 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.00419 0.81051 0.00138 0.0994 0.9936 0.81523 0.4397 0.5459 29 88 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-09 Undetermined Adult Trunk Surface Structure
65594 65594 SRR15390208 SRX11692437 SRS9724034 SRP331755 PRJNA753151 scRNA seq of fin and body zebrafish melanocytes GSE181748 Transcriptome Analysis Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body whereas the acral subtype arises on the palms of the hands soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes compared to body melanocytes revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma which was generated by injecting Casper fish with MniCoopR GFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total GFP+ body cells GFP body cells GFP+ fin cells GFP fin cells. Data was then analyzed and pooled together …   pubmed:35355015   XBN GSM5510265   source name:Zebrafish body skin|model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Body|cell type:GFP XBN Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao Hao et al. 2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija 2019. Principal component analysis Joliffe 1986 and UMAP dimensionality reduction McInnes 2018 were performed using default parameters with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al. 2020; Hunter Moncada et al. 2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output Zebrafish body skin   Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics   model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Body|cell type:GFP GSM5510265 GSM5510265: XBN; Danio rerio; RNA Seq GSM5510265   1 Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics GEO Accession:GSM5510265 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP331755     2387_XBN_IGO_11718_6_S6_L002_R1_001.fastq.gz 2387_XBN_IGO_11718_6_S6_L002_R2_001.fastq.gz fastq fastq 19057747059.0 162886727.0 GSM5510265 r2 0:29 1:88 A:5220986791;C:4370566015;G:4433233229;T:5032336069;N:624955 29 88     5220986791 4370566015 4433233229 5032336069 624955 SRX11692437 SRS9724034 SRA1274997 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.00434 0.81103 0.00156 0.09907 0.99417 0.81274 0.44052 0.54695 29 88 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-09 Undetermined Adult Trunk Surface Structure
65595 65595 SRR15390205 SRX11692435 SRS9724032 SRP331755 PRJNA753151 scRNA seq of fin and body zebrafish melanocytes GSE181748 Transcriptome Analysis Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body whereas the acral subtype arises on the palms of the hands soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes compared to body melanocytes revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma which was generated by injecting Casper fish with MniCoopR GFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total GFP+ body cells GFP body cells GFP+ fin cells GFP fin cells. Data was then analyzed and pooled together …   pubmed:35355015   XBG GSM5510264   source name:Zebrafish body skin|model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Body|cell type:GFP+ XBG Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao Hao et al. 2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija 2019. Principal component analysis Joliffe 1986 and UMAP dimensionality reduction McInnes 2018 were performed using default parameters with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al. 2020; Hunter Moncada et al. 2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output Zebrafish body skin   Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics   model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Body|cell type:GFP+ GSM5510264 GSM5510264: XBG; Danio rerio; RNA Seq GSM5510264   1 Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics GEO Accession:GSM5510264 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP331755     2386_XBG_IGO_11718_5_S5_L001_R1_001.fastq.gz 2386_XBG_IGO_11718_5_S5_L001_R2_001.fastq.gz fastq fastq 21756379320.0 185951960.0 GSM5510264 r1 0:29 1:88 A:6175271825;C:4793640120;G:4981225446;T:5805505185;N:736744 29 88     6175271825 4793640120 4981225446 5805505185 736744 SRX11692435 SRS9724032 SRA1274997 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.00899 0.8935 0.00261 0.14469 0.99056 0.79849 0.434 0.5426 29 88 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-09 Undetermined Adult Trunk Surface Structure
65596 65596 SRR15390206 SRX11692435 SRS9724032 SRP331755 PRJNA753151 scRNA seq of fin and body zebrafish melanocytes GSE181748 Transcriptome Analysis Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body whereas the acral subtype arises on the palms of the hands soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes compared to body melanocytes revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma which was generated by injecting Casper fish with MniCoopR GFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total GFP+ body cells GFP body cells GFP+ fin cells GFP fin cells. Data was then analyzed and pooled together …   pubmed:35355015   XBG GSM5510264   source name:Zebrafish body skin|model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Body|cell type:GFP+ XBG Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao Hao et al. 2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija 2019. Principal component analysis Joliffe 1986 and UMAP dimensionality reduction McInnes 2018 were performed using default parameters with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al. 2020; Hunter Moncada et al. 2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output Zebrafish body skin   Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics   model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Body|cell type:GFP+ GSM5510264 GSM5510264: XBG; Danio rerio; RNA Seq GSM5510264   1 Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics GEO Accession:GSM5510264 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP331755     2386_XBG_IGO_11718_5_S5_L002_R1_001.fastq.gz 2386_XBG_IGO_11718_5_S5_L002_R2_001.fastq.gz fastq fastq 21271780062.0 181810086.0 GSM5510264 r2 0:29 1:88 A:6043225103;C:4683532253;G:4864212050;T:5680108261;N:702395 29 88     6043225103 4683532253 4864212050 5680108261 702395 SRX11692435 SRS9724032 SRA1274997 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.00858 0.89419 0.00266 0.14661 0.99034 0.79622 0.39545 0.56688 29 88 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-09 Undetermined Adult Trunk Surface Structure
66178 66178 SRR15964630 SRX12254437 SRS10230009 SRP337784 PRJNA764519 Single Cell Analysis of adult zebrafish jaw joint GSE184403 Transcriptome Analysis To profile the diversity of cell types present in adult zebrafish synovial joints we performed single cell RNA sequencing of the uninjured adult jaw joint and identified multiple skeletal connective tissue and fibroblast subtypes including a joint specific periosteal population. Overall design: Single cell RNA sequencing of FACS isolated zebrafish joint cells trps1:eGFP enriched; sox10:DsRed enriched from 3 mpf microdissected jaw joints   pubmed:35127702   trps1:eGFP enriched GSM5587035   source name:Adult Jaw Joint|cell type:trps1:eGFP positive joint cell|age:3 mpf|tissue:Jaw joint trps1:eGFP enriched Fastq files were aligned using CellRanger v3.0.0 to GRCz11 built with v4.3.2.gtf including GFP and DsRed sequences as additional artificial chromosomes Genome build: z11 Supplementary files format and content: barcodes features and matrix files from Cell Ranger alignment Adult Jaw Joint   50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol   cell type:trps1:eGFP positive joint cell|age:3 mpf|tissue:Jaw joint GSM5587035 GSM5587035: trps1:eGFP enriched; Danio rerio; RNA Seq GSM5587035   1 50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol GEO Accession:GSM5587035 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP337784     trps1enriched-1_R1_001.fastq.gz trps1enriched-1_R2_001.fastq.gz fastq fastq 21524957734.0 145963727.0 GSM5587035 r1 0:27 1:120.47 A:6080775237;C:4508264559;G:4702878554;T:6215461741;N:17577643 27 120     6080775237 4508264559 4702878554 6215461741 17577643 SRX12254437 SRS10230009 SRA1296796 GEO Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center 2 0.00341 0.91093 0.00112 0.14627 0.99391 0.85693 0.46102 0.48941 27 121 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-19 Adult Adult Jaw Surface Structure
66179 66179 SRR15964631 SRX12254437 SRS10230009 SRP337784 PRJNA764519 Single Cell Analysis of adult zebrafish jaw joint GSE184403 Transcriptome Analysis To profile the diversity of cell types present in adult zebrafish synovial joints we performed single cell RNA sequencing of the uninjured adult jaw joint and identified multiple skeletal connective tissue and fibroblast subtypes including a joint specific periosteal population. Overall design: Single cell RNA sequencing of FACS isolated zebrafish joint cells trps1:eGFP enriched; sox10:DsRed enriched from 3 mpf microdissected jaw joints   pubmed:35127702   trps1:eGFP enriched GSM5587035   source name:Adult Jaw Joint|cell type:trps1:eGFP positive joint cell|age:3 mpf|tissue:Jaw joint trps1:eGFP enriched Fastq files were aligned using CellRanger v3.0.0 to GRCz11 built with v4.3.2.gtf including GFP and DsRed sequences as additional artificial chromosomes Genome build: z11 Supplementary files format and content: barcodes features and matrix files from Cell Ranger alignment Adult Jaw Joint   50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol   cell type:trps1:eGFP positive joint cell|age:3 mpf|tissue:Jaw joint GSM5587035 GSM5587035: trps1:eGFP enriched; Danio rerio; RNA Seq GSM5587035   1 50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol GEO Accession:GSM5587035 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP337784     trps1enriched-2_R1_001.fastq.gz trps1enriched-2_R2_001.fastq.gz fastq fastq 29538626136.0 200298691.0 GSM5587035 r2 0:27 1:120.47 A:8358449730;C:6152852316;G:6409091874;T:8594034218;N:24197998 27 120     8358449730 6152852316 6409091874 8594034218 24197998 SRX12254437 SRS10230009 SRA1296796 GEO Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center 2 0.00359 0.90985 0.00119 0.14958 0.99338 0.85878 0.42675 0.48789 27 118 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-19 Adult Adult Jaw Surface Structure
66180 66180 SRR15964632 SRX12254437 SRS10230009 SRP337784 PRJNA764519 Single Cell Analysis of adult zebrafish jaw joint GSE184403 Transcriptome Analysis To profile the diversity of cell types present in adult zebrafish synovial joints we performed single cell RNA sequencing of the uninjured adult jaw joint and identified multiple skeletal connective tissue and fibroblast subtypes including a joint specific periosteal population. Overall design: Single cell RNA sequencing of FACS isolated zebrafish joint cells trps1:eGFP enriched; sox10:DsRed enriched from 3 mpf microdissected jaw joints   pubmed:35127702   trps1:eGFP enriched GSM5587035   source name:Adult Jaw Joint|cell type:trps1:eGFP positive joint cell|age:3 mpf|tissue:Jaw joint trps1:eGFP enriched Fastq files were aligned using CellRanger v3.0.0 to GRCz11 built with v4.3.2.gtf including GFP and DsRed sequences as additional artificial chromosomes Genome build: z11 Supplementary files format and content: barcodes features and matrix files from Cell Ranger alignment Adult Jaw Joint   50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol   cell type:trps1:eGFP positive joint cell|age:3 mpf|tissue:Jaw joint GSM5587035 GSM5587035: trps1:eGFP enriched; Danio rerio; RNA Seq GSM5587035   1 50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol GEO Accession:GSM5587035 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP337784     trps1enriched-3_R1_001.fastq.gz trps1enriched-3_R2_001.fastq.gz fastq fastq 18834117972.0 127723979.0 GSM5587035 r3 0:27 1:120.46 A:5321823966;C:3931395608;G:4123902269;T:5441824191;N:15171938 27 120     5321823966 3931395608 4123902269 5441824191 15171938 SRX12254437 SRS10230009 SRA1296796 GEO Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center 2 0.00356 0.91092 0.00098 0.1444 0.99308 0.85066 0.45652 0.50535 27 121 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-19 Adult Adult Jaw Surface Structure
66181 66181 SRR15964633 SRX12254437 SRS10230009 SRP337784 PRJNA764519 Single Cell Analysis of adult zebrafish jaw joint GSE184403 Transcriptome Analysis To profile the diversity of cell types present in adult zebrafish synovial joints we performed single cell RNA sequencing of the uninjured adult jaw joint and identified multiple skeletal connective tissue and fibroblast subtypes including a joint specific periosteal population. Overall design: Single cell RNA sequencing of FACS isolated zebrafish joint cells trps1:eGFP enriched; sox10:DsRed enriched from 3 mpf microdissected jaw joints   pubmed:35127702   trps1:eGFP enriched GSM5587035   source name:Adult Jaw Joint|cell type:trps1:eGFP positive joint cell|age:3 mpf|tissue:Jaw joint trps1:eGFP enriched Fastq files were aligned using CellRanger v3.0.0 to GRCz11 built with v4.3.2.gtf including GFP and DsRed sequences as additional artificial chromosomes Genome build: z11 Supplementary files format and content: barcodes features and matrix files from Cell Ranger alignment Adult Jaw Joint   50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol   cell type:trps1:eGFP positive joint cell|age:3 mpf|tissue:Jaw joint GSM5587035 GSM5587035: trps1:eGFP enriched; Danio rerio; RNA Seq GSM5587035   1 50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol GEO Accession:GSM5587035 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP337784     trps1enriched-4_R1_001.fastq.gz trps1enriched-4_R2_001.fastq.gz fastq fastq 24543217204.0 166435205.0 GSM5587035 r4 0:27 1:120.46 A:6923484050;C:5154357751;G:5378630657;T:7066659666;N:20085080 27 120     6923484050 5154357751 5378630657 7066659666 20085080 SRX12254437 SRS10230009 SRA1296796 GEO Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center 2 0.00342 0.91125 0.00108 0.1445 0.99385 0.85279 0.4379 0.5084 27 121 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-19 Adult Adult Jaw Surface Structure
66182 66182 SRR15964626 SRX12254436 SRS10230008 SRP337784 PRJNA764519 Single Cell Analysis of adult zebrafish jaw joint GSE184403 Transcriptome Analysis To profile the diversity of cell types present in adult zebrafish synovial joints we performed single cell RNA sequencing of the uninjured adult jaw joint and identified multiple skeletal connective tissue and fibroblast subtypes including a joint specific periosteal population. Overall design: Single cell RNA sequencing of FACS isolated zebrafish joint cells trps1:eGFP enriched; sox10:DsRed enriched from 3 mpf microdissected jaw joints   pubmed:35127702   sox10:DsRed enriched GSM5587034   source name:Adult Jaw Joint|cell type:sox10:DsRed positive joint cell|age:3 mpf|tissue:Jaw joint sox10:DsRed enriched Fastq files were aligned using CellRanger v3.0.0 to GRCz11 built with v4.3.2.gtf including GFP and DsRed sequences as additional artificial chromosomes Genome build: z11 Supplementary files format and content: barcodes features and matrix files from Cell Ranger alignment Adult Jaw Joint   50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol   cell type:sox10:DsRed positive joint cell|age:3 mpf|tissue:Jaw joint GSM5587034 GSM5587034: sox10:DsRed enriched; Danio rerio; RNA Seq GSM5587034   1 50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol GEO Accession:GSM5587034 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP337784     sox10enriched-1_R1_001.fastq.gz sox10enriched-1_R2_001.fastq.gz fastq fastq 2310039840.0 15674545.0 GSM5587034 r1 0:27 1:120.38 A:657104627;C:477823382;G:502418027;T:670802267;N:1891537 27 120     657104627 477823382 502418027 670802267 1891537 SRX12254436 SRS10230008 SRA1296796 GEO Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center 2 0.00331 0.90804 0.00124 0.19789 0.99385 0.84918 0.5 0.4965 27 119 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-19 Adult Adult Jaw Surface Structure
66183 66183 SRR15964627 SRX12254436 SRS10230008 SRP337784 PRJNA764519 Single Cell Analysis of adult zebrafish jaw joint GSE184403 Transcriptome Analysis To profile the diversity of cell types present in adult zebrafish synovial joints we performed single cell RNA sequencing of the uninjured adult jaw joint and identified multiple skeletal connective tissue and fibroblast subtypes including a joint specific periosteal population. Overall design: Single cell RNA sequencing of FACS isolated zebrafish joint cells trps1:eGFP enriched; sox10:DsRed enriched from 3 mpf microdissected jaw joints   pubmed:35127702   sox10:DsRed enriched GSM5587034   source name:Adult Jaw Joint|cell type:sox10:DsRed positive joint cell|age:3 mpf|tissue:Jaw joint sox10:DsRed enriched Fastq files were aligned using CellRanger v3.0.0 to GRCz11 built with v4.3.2.gtf including GFP and DsRed sequences as additional artificial chromosomes Genome build: z11 Supplementary files format and content: barcodes features and matrix files from Cell Ranger alignment Adult Jaw Joint   50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol   cell type:sox10:DsRed positive joint cell|age:3 mpf|tissue:Jaw joint GSM5587034 GSM5587034: sox10:DsRed enriched; Danio rerio; RNA Seq GSM5587034   1 50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol GEO Accession:GSM5587034 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP337784     sox10enriched-2_R1_001.fastq.gz sox10enriched-2_R2_001.fastq.gz fastq fastq 2268301929.0 15392389.0 GSM5587034 r2 0:27 1:120.37 A:645886696;C:468225565;G:493153165;T:659172922;N:1863581 27 120     645886696 468225565 493153165 659172922 1863581 SRX12254436 SRS10230008 SRA1296796 GEO Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center 2 0.0032 0.90785 0.00116 0.19777 0.99423 0.84847 0.44783 0.49424 27 121 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-19 Adult Adult Jaw Surface Structure
66184 66184 SRR15964628 SRX12254436 SRS10230008 SRP337784 PRJNA764519 Single Cell Analysis of adult zebrafish jaw joint GSE184403 Transcriptome Analysis To profile the diversity of cell types present in adult zebrafish synovial joints we performed single cell RNA sequencing of the uninjured adult jaw joint and identified multiple skeletal connective tissue and fibroblast subtypes including a joint specific periosteal population. Overall design: Single cell RNA sequencing of FACS isolated zebrafish joint cells trps1:eGFP enriched; sox10:DsRed enriched from 3 mpf microdissected jaw joints   pubmed:35127702   sox10:DsRed enriched GSM5587034   source name:Adult Jaw Joint|cell type:sox10:DsRed positive joint cell|age:3 mpf|tissue:Jaw joint sox10:DsRed enriched Fastq files were aligned using CellRanger v3.0.0 to GRCz11 built with v4.3.2.gtf including GFP and DsRed sequences as additional artificial chromosomes Genome build: z11 Supplementary files format and content: barcodes features and matrix files from Cell Ranger alignment Adult Jaw Joint   50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol   cell type:sox10:DsRed positive joint cell|age:3 mpf|tissue:Jaw joint GSM5587034 GSM5587034: sox10:DsRed enriched; Danio rerio; RNA Seq GSM5587034   1 50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol GEO Accession:GSM5587034 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP337784     sox10enriched-3_R1_001.fastq.gz sox10enriched-3_R2_001.fastq.gz fastq fastq 2826349266.0 19178616.0 GSM5587034 r3 0:27 1:120.37 A:803669086;C:587771264;G:615160821;T:817438779;N:2309316 27 120     803669086 587771264 615160821 817438779 2309316 SRX12254436 SRS10230008 SRA1296796 GEO Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center 2 0.00361 0.90664 0.00122 0.19569 0.99328 0.85173 0.44136 0.49393 27 121 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-19 Adult Adult Jaw Surface Structure
66185 66185 SRR15964629 SRX12254436 SRS10230008 SRP337784 PRJNA764519 Single Cell Analysis of adult zebrafish jaw joint GSE184403 Transcriptome Analysis To profile the diversity of cell types present in adult zebrafish synovial joints we performed single cell RNA sequencing of the uninjured adult jaw joint and identified multiple skeletal connective tissue and fibroblast subtypes including a joint specific periosteal population. Overall design: Single cell RNA sequencing of FACS isolated zebrafish joint cells trps1:eGFP enriched; sox10:DsRed enriched from 3 mpf microdissected jaw joints   pubmed:35127702   sox10:DsRed enriched GSM5587034   source name:Adult Jaw Joint|cell type:sox10:DsRed positive joint cell|age:3 mpf|tissue:Jaw joint sox10:DsRed enriched Fastq files were aligned using CellRanger v3.0.0 to GRCz11 built with v4.3.2.gtf including GFP and DsRed sequences as additional artificial chromosomes Genome build: z11 Supplementary files format and content: barcodes features and matrix files from Cell Ranger alignment Adult Jaw Joint   50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol   cell type:sox10:DsRed positive joint cell|age:3 mpf|tissue:Jaw joint GSM5587034 GSM5587034: sox10:DsRed enriched; Danio rerio; RNA Seq GSM5587034   1 50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol GEO Accession:GSM5587034 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP337784     sox10enriched-4_R1_001.fastq.gz sox10enriched-4_R2_001.fastq.gz fastq fastq 2932941460.0 19904579.0 GSM5587034 r4 0:27 1:120.35 A:832669575;C:611997497;G:644091515;T:841813951;N:2368922 27 120     832669575 611997497 644091515 841813951 2368922 SRX12254436 SRS10230008 SRA1296796 GEO Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center 2 0.00343 0.91021 0.00112 0.19104 0.99375 0.84883 0.49557 0.50272 27 121 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-19 Adult Adult Jaw Surface Structure
66719 66719 SRR16490785 SRX12693895 SRS10644777 SRP342165 PRJNA772761 Single cell transcriptomics reveals critical molecular programming of progenitors for motor neurons and oligodendrocytes in zebrafish GSE186163 Transcriptome Analysis pmn progenitors and their offspring in spinal cords are isolated for sc RNAseq Overall design: olig2+ cells were isolated from the trunks of Tgolig2:dsred by FACS and underwent scRNA seq   pubmed:36063998   olig2+ cells in zebrafish trunks 60hpf GSM5639644   source name:Tgolig2:dsred trunks|Stage:60 hpf|genotype:Tg olig2:dsred|tissue:trunk olig2+ cells in zebrafish trunks 60hpf Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Genes detectable in more than two cells were defined as “expressed”. Cells with <1000 genes detected were removed. Counts were normalized to 10000 and transformed into logarithmic scales. A neighborhood graph was embedded using UMAP displaying the top 4000 highly variable genes across cells. Cells were clustered by the Louvain Algorithm. The trajectory interface of all cell clusters was done using the layout 'fa'. These analyses were performed by the Python based SCANPY package Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Tgolig2:dsred trunks   Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell 3’ Library and Gel Bead kit V3   Stage:60 hpf|genotype:Tg olig2:dsred|tissue:trunk GSM5639644 GSM5639644: olig2+ cells in zebrafish trunks 60hpf; Danio rerio; RNA Seq GSM5639644 r1 GSM5639644 1 Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell three prime Library and Gel Bead kit V3   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP342165     200326C_z60hpf_S1_L001_R1_001.fastq.gz 200326C_z60hpf_S1_L001_R2_001.fastq.gz fastq fastq 27364318800.0 91214396.0 GSM5639644 r1 0:150 1:150 A:10071536495;C:5175486957;G:4924076777;T:7192804284;N:414287 150 150     10071536495 5175486957 4924076777 7192804284 414287 SRX12693895 SRS10644777 SRA1322635 Nantong University Nantong University 2 0.0 0.90895 0.0 0.13505 1.0 0.79797   0.51047 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2021-10-19 Hatching Embryo Trunk Surface Structure
66720 66720 SRR16490786 SRX12693895 SRS10644777 SRP342165 PRJNA772761 Single cell transcriptomics reveals critical molecular programming of progenitors for motor neurons and oligodendrocytes in zebrafish GSE186163 Transcriptome Analysis pmn progenitors and their offspring in spinal cords are isolated for sc RNAseq Overall design: olig2+ cells were isolated from the trunks of Tgolig2:dsred by FACS and underwent scRNA seq   pubmed:36063998   olig2+ cells in zebrafish trunks 60hpf GSM5639644   source name:Tgolig2:dsred trunks|Stage:60 hpf|genotype:Tg olig2:dsred|tissue:trunk olig2+ cells in zebrafish trunks 60hpf Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Genes detectable in more than two cells were defined as “expressed”. Cells with <1000 genes detected were removed. Counts were normalized to 10000 and transformed into logarithmic scales. A neighborhood graph was embedded using UMAP displaying the top 4000 highly variable genes across cells. Cells were clustered by the Louvain Algorithm. The trajectory interface of all cell clusters was done using the layout 'fa'. These analyses were performed by the Python based SCANPY package Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Tgolig2:dsred trunks   Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell 3’ Library and Gel Bead kit V3   Stage:60 hpf|genotype:Tg olig2:dsred|tissue:trunk GSM5639644 GSM5639644: olig2+ cells in zebrafish trunks 60hpf; Danio rerio; RNA Seq GSM5639644 r1 GSM5639644 1 Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell three prime Library and Gel Bead kit V3   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP342165     200326C_z60hpf_S1_L002_R1_001.fastq.gz 200326C_z60hpf_S1_L002_R2_001.fastq.gz fastq fastq 25135796400.0 83785988.0 GSM5639644 r2 0:150 1:150 A:9233555166;C:4754173569;G:4523141240;T:6624550958;N:375467 150 150     9233555166 4754173569 4523141240 6624550958 375467 SRX12693895 SRS10644777 SRA1322635 Nantong University Nantong University 2 0.0 0.91014 0.0 0.13408 1.0 0.79805   0.50682 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2021-10-19 Hatching Embryo Trunk Surface Structure
66721 66721 SRR16490787 SRX12693895 SRS10644777 SRP342165 PRJNA772761 Single cell transcriptomics reveals critical molecular programming of progenitors for motor neurons and oligodendrocytes in zebrafish GSE186163 Transcriptome Analysis pmn progenitors and their offspring in spinal cords are isolated for sc RNAseq Overall design: olig2+ cells were isolated from the trunks of Tgolig2:dsred by FACS and underwent scRNA seq   pubmed:36063998   olig2+ cells in zebrafish trunks 60hpf GSM5639644   source name:Tgolig2:dsred trunks|Stage:60 hpf|genotype:Tg olig2:dsred|tissue:trunk olig2+ cells in zebrafish trunks 60hpf Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Genes detectable in more than two cells were defined as “expressed”. Cells with <1000 genes detected were removed. Counts were normalized to 10000 and transformed into logarithmic scales. A neighborhood graph was embedded using UMAP displaying the top 4000 highly variable genes across cells. Cells were clustered by the Louvain Algorithm. The trajectory interface of all cell clusters was done using the layout 'fa'. These analyses were performed by the Python based SCANPY package Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Tgolig2:dsred trunks   Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell 3’ Library and Gel Bead kit V3   Stage:60 hpf|genotype:Tg olig2:dsred|tissue:trunk GSM5639644 GSM5639644: olig2+ cells in zebrafish trunks 60hpf; Danio rerio; RNA Seq GSM5639644 r1 GSM5639644 1 Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell three prime Library and Gel Bead kit V3   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP342165     200326C_z60hpf_S1_L003_R1_001.fastq.gz 200326C_z60hpf_S1_L003_R2_001.fastq.gz fastq fastq 26660624700.0 88868749.0 GSM5639644 r3 0:150 1:150 A:9806302304;C:5038591446;G:4797994616;T:7017333749;N:402585 150 150     9806302304 5038591446 4797994616 7017333749 402585 SRX12693895 SRS10644777 SRA1322635 Nantong University Nantong University 2 0.0 0.90794 0.0 0.13331 1.0 0.79981   0.50544 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2021-10-19 Hatching Embryo Trunk Surface Structure
66722 66722 SRR16490788 SRX12693895 SRS10644777 SRP342165 PRJNA772761 Single cell transcriptomics reveals critical molecular programming of progenitors for motor neurons and oligodendrocytes in zebrafish GSE186163 Transcriptome Analysis pmn progenitors and their offspring in spinal cords are isolated for sc RNAseq Overall design: olig2+ cells were isolated from the trunks of Tgolig2:dsred by FACS and underwent scRNA seq   pubmed:36063998   olig2+ cells in zebrafish trunks 60hpf GSM5639644   source name:Tgolig2:dsred trunks|Stage:60 hpf|genotype:Tg olig2:dsred|tissue:trunk olig2+ cells in zebrafish trunks 60hpf Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Genes detectable in more than two cells were defined as “expressed”. Cells with <1000 genes detected were removed. Counts were normalized to 10000 and transformed into logarithmic scales. A neighborhood graph was embedded using UMAP displaying the top 4000 highly variable genes across cells. Cells were clustered by the Louvain Algorithm. The trajectory interface of all cell clusters was done using the layout 'fa'. These analyses were performed by the Python based SCANPY package Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Tgolig2:dsred trunks   Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell 3’ Library and Gel Bead kit V3   Stage:60 hpf|genotype:Tg olig2:dsred|tissue:trunk GSM5639644 GSM5639644: olig2+ cells in zebrafish trunks 60hpf; Danio rerio; RNA Seq GSM5639644 r1 GSM5639644 1 Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell three prime Library and Gel Bead kit V3   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP342165     200326C_z60hpf_S1_L004_R1_001.fastq.gz 200326C_z60hpf_S1_L004_R2_001.fastq.gz fastq fastq 26473468500.0 88244895.0 GSM5639644 r4 0:150 1:150 A:9733096090;C:5005227733;G:4764331985;T:6970420076;N:392616 150 150     9733096090 5005227733 4764331985 6970420076 392616 SRX12693895 SRS10644777 SRA1322635 Nantong University Nantong University 2 0.0 0.90896 0.0 0.13496 1.0 0.79817   0.51059 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2021-10-19 Hatching Embryo Trunk Surface Structure
66723 66723 SRR16490789 SRX12693894 SRS10644776 SRP342165 PRJNA772761 Single cell transcriptomics reveals critical molecular programming of progenitors for motor neurons and oligodendrocytes in zebrafish GSE186163 Transcriptome Analysis pmn progenitors and their offspring in spinal cords are isolated for sc RNAseq Overall design: olig2+ cells were isolated from the trunks of Tgolig2:dsred by FACS and underwent scRNA seq   pubmed:36063998   olig2+ cells in zebrafish trunks 28hpf GSM5639643   source name:Tgolig2:dsred trunks|Stage:28 hpf|genotype:Tg olig2:dsred|tissue:trunk olig2+ cells in zebrafish trunks 28hpf Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Genes detectable in more than two cells were defined as “expressed”. Cells with <1000 genes detected were removed. Counts were normalized to 10000 and transformed into logarithmic scales. A neighborhood graph was embedded using UMAP displaying the top 4000 highly variable genes across cells. Cells were clustered by the Louvain Algorithm. The trajectory interface of all cell clusters was done using the layout 'fa'. These analyses were performed by the Python based SCANPY package Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Tgolig2:dsred trunks   Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell 3’ Library and Gel Bead kit V3   Stage:28 hpf|genotype:Tg olig2:dsred|tissue:trunk GSM5639643 GSM5639643: olig2+ cells in zebrafish trunks 28hpf; Danio rerio; RNA Seq GSM5639643 r1 GSM5639643 1 Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell three prime Library and Gel Bead kit V3   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP342165     200326C_z28hpf_S1_L001_R1_001.fastq.gz 200326C_z28hpf_S1_L001_R2_001.fastq.gz fastq fastq 17790840000.0 59302800.0 GSM5639643 r1 0:150 1:150 A:6396040437;C:3363869870;G:3210547721;T:4820107751;N:274221 150 150     6396040437 3363869870 3210547721 4820107751 274221 SRX12693894 SRS10644776 SRA1322635 Nantong University Nantong University 2 0.0 0.89269 0.0 0.14196 1.0 0.80998   0.49581 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2021-10-19 Pharyngula Embryo Trunk Surface Structure
66724 66724 SRR16490790 SRX12693894 SRS10644776 SRP342165 PRJNA772761 Single cell transcriptomics reveals critical molecular programming of progenitors for motor neurons and oligodendrocytes in zebrafish GSE186163 Transcriptome Analysis pmn progenitors and their offspring in spinal cords are isolated for sc RNAseq Overall design: olig2+ cells were isolated from the trunks of Tgolig2:dsred by FACS and underwent scRNA seq   pubmed:36063998   olig2+ cells in zebrafish trunks 28hpf GSM5639643   source name:Tgolig2:dsred trunks|Stage:28 hpf|genotype:Tg olig2:dsred|tissue:trunk olig2+ cells in zebrafish trunks 28hpf Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Genes detectable in more than two cells were defined as “expressed”. Cells with <1000 genes detected were removed. Counts were normalized to 10000 and transformed into logarithmic scales. A neighborhood graph was embedded using UMAP displaying the top 4000 highly variable genes across cells. Cells were clustered by the Louvain Algorithm. The trajectory interface of all cell clusters was done using the layout 'fa'. These analyses were performed by the Python based SCANPY package Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Tgolig2:dsred trunks   Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell 3’ Library and Gel Bead kit V3   Stage:28 hpf|genotype:Tg olig2:dsred|tissue:trunk GSM5639643 GSM5639643: olig2+ cells in zebrafish trunks 28hpf; Danio rerio; RNA Seq GSM5639643 r1 GSM5639643 1 Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell three prime Library and Gel Bead kit V3   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP342165     200326C_z28hpf_S1_L002_R1_001.fastq.gz 200326C_z28hpf_S1_L002_R2_001.fastq.gz fastq fastq 25907915400.0 86359718.0 GSM5639643 r2 0:150 1:150 A:9312085267;C:4909235081;G:4679112677;T:7007080032;N:402343 150 150     9312085267 4909235081 4679112677 7007080032 402343 SRX12693894 SRS10644776 SRA1322635 Nantong University Nantong University 2 0.0 0.89826 0.0 0.14235 1.0 0.80949   0.50368 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2021-10-19 Pharyngula Embryo Trunk Surface Structure
66725 66725 SRR16490791 SRX12693894 SRS10644776 SRP342165 PRJNA772761 Single cell transcriptomics reveals critical molecular programming of progenitors for motor neurons and oligodendrocytes in zebrafish GSE186163 Transcriptome Analysis pmn progenitors and their offspring in spinal cords are isolated for sc RNAseq Overall design: olig2+ cells were isolated from the trunks of Tgolig2:dsred by FACS and underwent scRNA seq   pubmed:36063998   olig2+ cells in zebrafish trunks 28hpf GSM5639643   source name:Tgolig2:dsred trunks|Stage:28 hpf|genotype:Tg olig2:dsred|tissue:trunk olig2+ cells in zebrafish trunks 28hpf Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Genes detectable in more than two cells were defined as “expressed”. Cells with <1000 genes detected were removed. Counts were normalized to 10000 and transformed into logarithmic scales. A neighborhood graph was embedded using UMAP displaying the top 4000 highly variable genes across cells. Cells were clustered by the Louvain Algorithm. The trajectory interface of all cell clusters was done using the layout 'fa'. These analyses were performed by the Python based SCANPY package Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Tgolig2:dsred trunks   Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell 3’ Library and Gel Bead kit V3   Stage:28 hpf|genotype:Tg olig2:dsred|tissue:trunk GSM5639643 GSM5639643: olig2+ cells in zebrafish trunks 28hpf; Danio rerio; RNA Seq GSM5639643 r1 GSM5639643 1 Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell three prime Library and Gel Bead kit V3   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP342165     200326C_z28hpf_S1_L003_R1_001.fastq.gz 200326C_z28hpf_S1_L003_R2_001.fastq.gz fastq fastq 22487485800.0 74958286.0 GSM5639643 r3 0:150 1:150 A:8079631079;C:4246853980;G:4058165201;T:6102481857;N:353683 150 150     8079631079 4246853980 4058165201 6102481857 353683 SRX12693894 SRS10644776 SRA1322635 Nantong University Nantong University 2 0.0 0.89773 0.0 0.14164 1.0 0.80827   0.50003 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2021-10-19 Pharyngula Embryo Trunk Surface Structure
66726 66726 SRR16490792 SRX12693894 SRS10644776 SRP342165 PRJNA772761 Single cell transcriptomics reveals critical molecular programming of progenitors for motor neurons and oligodendrocytes in zebrafish GSE186163 Transcriptome Analysis pmn progenitors and their offspring in spinal cords are isolated for sc RNAseq Overall design: olig2+ cells were isolated from the trunks of Tgolig2:dsred by FACS and underwent scRNA seq   pubmed:36063998   olig2+ cells in zebrafish trunks 28hpf GSM5639643   source name:Tgolig2:dsred trunks|Stage:28 hpf|genotype:Tg olig2:dsred|tissue:trunk olig2+ cells in zebrafish trunks 28hpf Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Genes detectable in more than two cells were defined as “expressed”. Cells with <1000 genes detected were removed. Counts were normalized to 10000 and transformed into logarithmic scales. A neighborhood graph was embedded using UMAP displaying the top 4000 highly variable genes across cells. Cells were clustered by the Louvain Algorithm. The trajectory interface of all cell clusters was done using the layout 'fa'. These analyses were performed by the Python based SCANPY package Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Tgolig2:dsred trunks   Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell 3’ Library and Gel Bead kit V3   Stage:28 hpf|genotype:Tg olig2:dsred|tissue:trunk GSM5639643 GSM5639643: olig2+ cells in zebrafish trunks 28hpf; Danio rerio; RNA Seq GSM5639643 r1 GSM5639643 1 Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell three prime Library and Gel Bead kit V3   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP342165     200326C_z28hpf_S1_L004_R1_001.fastq.gz 200326C_z28hpf_S1_L004_R2_001.fastq.gz fastq fastq 22801608900.0 76005363.0 GSM5639643 r4 0:150 1:150 A:8194753928;C:4313659172;G:4114764638;T:6178079087;N:352075 150 150     8194753928 4313659172 4114764638 6178079087 352075 SRX12693894 SRS10644776 SRA1322635 Nantong University Nantong University 2 0.0 0.89811 0.0 0.14101 1.0 0.80618   0.4925 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2021-10-19 Pharyngula Embryo Trunk Surface Structure
66757 66757 SRR23717090 SRX19578259 SRS16961241 SRP342737 PRJNA773778 Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.STRT seq] GSE186425 Other Using a combination of single cell multi omics lineage tracing and functional assays we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population but where and how HSPC heterogeneity occurs remain unclear. Here we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency we performed scRNA seq with the sorted ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. parent bioproject:PRJNA773771 pubmed:37016019   DP1 36hpf GSM7083138   source name:Zebrafish trunk region|tissue:Zebrafish trunk region 36hpf|cells:single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells|Stage:36 hpf loc name:missing|collection date:missing DP1 36hpf For scRNA seq and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters using the GRCz11 reference genome. For STRT seq raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates MACS2 was used for the peak calling. Assembly: GRCz11 Library strategy: STRT seq Zebrafish trunk region   For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepared according to Hyp…   tissue:Zebrafish trunk region 36hpf|cells:single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells|Stage:36 hpf GSM7083138 GSM7083138: DP1 36hpf; Danio rerio; OTHER GSM7083138 r1 GSM7083138 1 For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepare…   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP342737     36hpf-DP1_FKDL202627688-1a_1.raw.fq.gz 36hpf-DP1_FKDL202627688-1a_2.raw.fq.gz fastq fastq 36641999100.0 122139997.0 GSM7083138 r1 0:150 1:150 A:11840633171;C:5285812067;G:6638992204;T:12876249105;N:312553 150 150     11840633171 5285812067 6638992204 12876249105 312553 SRX19578259 SRS16961241 SRA1600575 Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES 2 0.8912 0.01571 0.09673 0.00653 0.86145 0.99849 0.61834 0.72033 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2023-03-06 Pharyngula Embryo Trunk Surface Structure
66758 66758 SRR23717091 SRX19578258 SRS16961240 SRP342737 PRJNA773778 Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.STRT seq] GSE186425 Other Using a combination of single cell multi omics lineage tracing and functional assays we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population but where and how HSPC heterogeneity occurs remain unclear. Here we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency we performed scRNA seq with the sorted ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. parent bioproject:PRJNA773771 pubmed:37016019   DP2 36hpf GSM7083139   source name:Zebrafish trunk region|tissue:Zebrafish trunk region 36hpf|cells:single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells|Stage:36 hpf loc name:missing|collection date:missing DP2 36hpf For scRNA seq and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters using the GRCz11 reference genome. For STRT seq raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates MACS2 was used for the peak calling. Assembly: GRCz11 Library strategy: STRT seq Zebrafish trunk region   For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepared according to Hyp…   tissue:Zebrafish trunk region 36hpf|cells:single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells|Stage:36 hpf GSM7083139 GSM7083139: DP2 36hpf; Danio rerio; OTHER GSM7083139 r1 GSM7083139 1 For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepare…   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP342737     36hpf-DP2_FKDL202627692-1a_1.raw.fq.gz 36hpf-DP2_FKDL202627692-1a_2.raw.fq.gz fastq fastq 45339599100.0 151131997.0 GSM7083139 r1 0:150 1:150 A:14092451998;C:7125629842;G:9985822921;T:14135305628;N:388711 150 150     14092451998 7125629842 9985822921 14135305628 388711 SRX19578258 SRS16961240 SRA1600575 Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES 2 0.79702 0.00323 0.08737 0.00105 0.88663 0.99882 0.62618 0.6 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2023-03-06 Pharyngula Embryo Trunk Surface Structure
66759 66759 SRR23717092 SRX19578257 SRS16961239 SRP342737 PRJNA773778 Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.STRT seq] GSE186425 Other Using a combination of single cell multi omics lineage tracing and functional assays we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population but where and how HSPC heterogeneity occurs remain unclear. Here we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency we performed scRNA seq with the sorted ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. parent bioproject:PRJNA773771 pubmed:37016019   SP 36hpf GSM7083140   source name:Zebrafish trunk region|tissue:Zebrafish trunk region 36hpf|cells:single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells|Stage:36 hpf loc name:missing|collection date:missing SP 36hpf For scRNA seq and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters using the GRCz11 reference genome. For STRT seq raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates MACS2 was used for the peak calling. Assembly: GRCz11 Library strategy: STRT seq Zebrafish trunk region   For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepared according to Hyp…   tissue:Zebrafish trunk region 36hpf|cells:single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells|Stage:36 hpf GSM7083140 GSM7083140: SP 36hpf; Danio rerio; OTHER GSM7083140 r1 GSM7083140 1 For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepare…   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP342737     36hpf-SP_FKDL202627693-1a_1.raw.fq.gz 36hpf-SP_FKDL202627693-1a_2.raw.fq.gz fastq fastq 44757872400.0 149192908.0 GSM7083140 r1 0:150 1:150 A:13194662551;C:6817138207;G:9879151250;T:14866177703;N:742689 150 150     13194662551 6817138207 9879151250 14866177703 742689 SRX19578257 SRS16961239 SRA1600575 Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES 2 0.7854 0.00221 0.062 0.00084 0.90995 0.99904 0.43661 0.67741 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2023-03-06 Pharyngula Embryo Trunk Surface Structure
67321 67321 SRR17117603 SRX13302172 SRS11213397 SRP349128 PRJNA785890 Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish GSE190115 Transcriptome Analysis To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration   pubmed:37021774   KIT Day10 GSM5714340   tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:10 KIT Day10 Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects Tgmitfa:nlsEGFP FACS enriched cells 750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age genotype:kitalf|day:10 GSM5714340 GSM5714340: KIT Day10; Danio rerio; RNA Seq GSM5714340 r1 GSM5714340 1 Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP349128   assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate KITD10_possorted_genome_bam.bam 10X Genomics bam file 13520056900.0 270401138.0 GSM5714340 r1 0:50 A:4003001263;C:2787125304;G:3034885371;T:3692995124;N:2049838 50       4003001263 2787125304 3034885371 3692995124 2049838 SRX13302172 SRS11213397 SRA1620868 Craig Ceol, Molecular Medicine, UMass Medical School Craig Ceol, Molecular Medicine, UMass Medical School 1 0.89988   0.15778   0.81779   0.55873   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-12-03 Adult Adult Skin Surface Structure
67322 67322 SRR17117604 SRX13302171 SRS11213396 SRP349128 PRJNA785890 Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish GSE190115 Transcriptome Analysis To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration   pubmed:37021774   KIT Day5 GSM5714339   tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:5 KIT Day5 Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects Tgmitfa:nlsEGFP FACS enriched cells 750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age genotype:kitalf|day:5 GSM5714339 GSM5714339: KIT Day5; Danio rerio; RNA Seq GSM5714339 r1 GSM5714339 1 Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP349128   assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate KITD5_possorted_genome_bam.bam 10X Genomics bam file 15339323300.0 306786466.0 GSM5714339 r1 0:50 A:4515134365;C:3259123747;G:3665791919;T:3898089485;N:1183784 50       4515134365 3259123747 3665791919 3898089485 1183784 SRX13302171 SRS11213396 SRA1620868 Craig Ceol, Molecular Medicine, UMass Medical School Craig Ceol, Molecular Medicine, UMass Medical School 1 0.90243   0.15706   0.80507   0.59995   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-12-03 Adult Adult Skin Surface Structure
67323 67323 SRR17117605 SRX13302170 SRS11213395 SRP349128 PRJNA785890 Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish GSE190115 Transcriptome Analysis To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration   pubmed:37021774   KIT Day3 2 GSM5714338   tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:3 KIT Day3 2 Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects Tgmitfa:nlsEGFP FACS enriched cells 750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age genotype:kitalf|day:3 GSM5714338 GSM5714338: KIT Day3 2; Danio rerio; RNA Seq GSM5714338 r1 GSM5714338 1 Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP349128   assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate KITD3B_possorted_genome_bam.bam 10X Genomics bam file 7025134450.0 140502689.0 GSM5714338 r1 0:50 A:2061820993;C:1482027410;G:1665199726;T:1810366819;N:5719502 50       2061820993 1482027410 1665199726 1810366819 5719502 SRX13302170 SRS11213395 SRA1620868 Craig Ceol, Molecular Medicine, UMass Medical School Craig Ceol, Molecular Medicine, UMass Medical School 1 0.90656   0.17308   0.80975   0.61461   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-12-03 Adult Adult Skin Surface Structure
67324 67324 SRR17117606 SRX13302169 SRS11213394 SRP349128 PRJNA785890 Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish GSE190115 Transcriptome Analysis To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration   pubmed:37021774   KIT Day3 1 GSM5714337   tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:3 KIT Day3 1 Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects Tgmitfa:nlsEGFP FACS enriched cells 750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age genotype:kitalf|day:3 GSM5714337 GSM5714337: KIT Day3 1; Danio rerio; RNA Seq GSM5714337 r1 GSM5714337 1 Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP349128   assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate KITD3A_possorted_genome_bam.bam 10X Genomics bam file 12309733350.0 246194667.0 GSM5714337 r1 0:50 A:3671780931;C:2604474006;G:3028253002;T:3001177496;N:4047915 50       3671780931 2604474006 3028253002 3001177496 4047915 SRX13302169 SRS11213394 SRA1620868 Craig Ceol, Molecular Medicine, UMass Medical School Craig Ceol, Molecular Medicine, UMass Medical School 1 0.8991   0.14599   0.82347   0.59507   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-12-03 Adult Adult Skin Surface Structure
67325 67325 SRR17117607 SRX13302168 SRS11213393 SRP349128 PRJNA785890 Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish GSE190115 Transcriptome Analysis To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration   pubmed:37021774   KIT Day2 GSM5714336   tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:2 KIT Day2 Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects Tgmitfa:nlsEGFP FACS enriched cells 750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age genotype:kitalf|day:2 GSM5714336 GSM5714336: KIT Day2; Danio rerio; RNA Seq GSM5714336 r1 GSM5714336 1 Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP349128   assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate KITD2_possorted_genome_bam.bam 10X Genomics bam file 12734582200.0 254691644.0 GSM5714336 r1 0:50 A:3752064713;C:2645000864;G:2866879156;T:3468673547;N:1963920 50       3752064713 2645000864 2866879156 3468673547 1963920 SRX13302168 SRS11213393 SRA1620868 Craig Ceol, Molecular Medicine, UMass Medical School Craig Ceol, Molecular Medicine, UMass Medical School 1 0.9007   0.15094   0.82601   0.58222   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-12-03 Adult Adult Skin Surface Structure
67326 67326 SRR17117608 SRX13302167 SRS11213392 SRP349128 PRJNA785890 Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish GSE190115 Transcriptome Analysis To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration   pubmed:37021774   KIT Day1 GSM5714335   tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:1 KIT Day1 Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects Tgmitfa:nlsEGFP FACS enriched cells 750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age genotype:kitalf|day:1 GSM5714335 GSM5714335: KIT Day1; Danio rerio; RNA Seq GSM5714335 r1 GSM5714335 1 Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP349128   assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate KITD1_possorted_genome_bam.bam 10X Genomics bam file 11105860850.0 222117217.0 GSM5714335 r1 0:50 A:3280343742;C:2367594246;G:2631026655;T:2823244720;N:3651487 50       3280343742 2367594246 2631026655 2823244720 3651487 SRX13302167 SRS11213392 SRA1620868 Craig Ceol, Molecular Medicine, UMass Medical School Craig Ceol, Molecular Medicine, UMass Medical School 1 0.91294   0.1651   0.81592   0.60997   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-12-03 Adult Adult Skin Surface Structure
67327 67327 SRR17117609 SRX13302166 SRS11213391 SRP349128 PRJNA785890 Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish GSE190115 Transcriptome Analysis To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration   pubmed:37021774   KIT day x GSM5714334   tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:0 KIT day x Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects Tgmitfa:nlsEGFP FACS enriched cells 750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age genotype:kitalf|day:0 GSM5714334 GSM5714334: KIT day x; Danio rerio; RNA Seq GSM5714334 r1 GSM5714334 1 Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP349128   assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate KITD0_possorted_genome_bam.bam 10X Genomics bam file 8896963450.0 177939269.0 GSM5714334 r1 0:50 A:2644408729;C:1877280130;G:2120951498;T:2253636691;N:686402 50       2644408729 1877280130 2120951498 2253636691 686402 SRX13302166 SRS11213391 SRA1620868 Craig Ceol, Molecular Medicine, UMass Medical School Craig Ceol, Molecular Medicine, UMass Medical School 1 0.90601   0.17428   0.8144   0.6019   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-12-03 Adult Adult Skin Surface Structure
67328 67328 SRR17117610 SRX13302165 SRS11213390 SRP349128 PRJNA785890 Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish GSE190115 Transcriptome Analysis To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration   pubmed:37021774   WT Day10 GSM5714333   tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:10 WT Day10 Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects Tgmitfa:nlsEGFP FACS enriched cells 750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age genotype:WT|day:10 GSM5714333 GSM5714333: WT Day10; Danio rerio; RNA Seq GSM5714333 r1 GSM5714333 1 Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP349128   assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate WTD10_possorted_genome_bam.bam 10X Genomics bam file 12279427400.0 245588548.0 GSM5714333 r1 0:50 A:3639861301;C:2609067706;G:2996068551;T:3030567477;N:3862365 50       3639861301 2609067706 2996068551 3030567477 3862365 SRX13302165 SRS11213390 SRA1620868 Craig Ceol, Molecular Medicine, UMass Medical School Craig Ceol, Molecular Medicine, UMass Medical School 1 0.90407   0.15949   0.83019   0.59401   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-12-03 Adult Adult Skin Surface Structure
67329 67329 SRR17117611 SRX13302164 SRS11213389 SRP349128 PRJNA785890 Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish GSE190115 Transcriptome Analysis To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration   pubmed:37021774   WT Day5 GSM5714332   tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:5 WT Day5 Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects Tgmitfa:nlsEGFP FACS enriched cells 750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age genotype:WT|day:5 GSM5714332 GSM5714332: WT Day5; Danio rerio; RNA Seq GSM5714332 r1 GSM5714332 1 Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP349128   assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate WTD5_possorted_genome_bam.bam 10X Genomics bam file 8474510800.0 169490216.0 GSM5714332 r1 0:50 A:2564658874;C:1701773199;G:1897587120;T:2308201539;N:2290068 50       2564658874 1701773199 1897587120 2308201539 2290068 SRX13302164 SRS11213389 SRA1620868 Craig Ceol, Molecular Medicine, UMass Medical School Craig Ceol, Molecular Medicine, UMass Medical School 1 0.89752   0.17262   0.8115   0.6036   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-12-03 Adult Adult Skin Surface Structure
67330 67330 SRR17117612 SRX13302163 SRS11213388 SRP349128 PRJNA785890 Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish GSE190115 Transcriptome Analysis To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration   pubmed:37021774   WT Day3 GSM5714331   tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:3 WT Day3 Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects Tgmitfa:nlsEGFP FACS enriched cells 750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age genotype:WT|day:3 GSM5714331 GSM5714331: WT Day3; Danio rerio; RNA Seq GSM5714331 r1 GSM5714331 1 Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP349128   assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate WTD3_possorted_genome_bam.bam 10X Genomics bam file 9051704300.0 181034086.0 GSM5714331 r1 0:50 A:2665138947;C:1946161834;G:2211744115;T:2225805018;N:2854386 50       2665138947 1946161834 2211744115 2225805018 2854386 SRX13302163 SRS11213388 SRA1620868 Craig Ceol, Molecular Medicine, UMass Medical School Craig Ceol, Molecular Medicine, UMass Medical School 1 0.90675   0.14473   0.81884   0.58208   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-12-03 Adult Adult Skin Surface Structure
67331 67331 SRR17117613 SRX13302162 SRS11213387 SRP349128 PRJNA785890 Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish GSE190115 Transcriptome Analysis To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration   pubmed:37021774   WT Day2 GSM5714330   tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:2 WT Day2 Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects Tgmitfa:nlsEGFP FACS enriched cells 750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age genotype:WT|day:2 GSM5714330 GSM5714330: WT Day2; Danio rerio; RNA Seq GSM5714330 r1 GSM5714330 1 Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP349128   assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate WTD2_possorted_genome_bam.bam 10X Genomics bam file 14707462000.0 294149240.0 GSM5714330 r1 0:50 A:4299212743;C:3141543121;G:3608335320;T:3651134459;N:7236357 50       4299212743 3141543121 3608335320 3651134459 7236357 SRX13302162 SRS11213387 SRA1620868 Craig Ceol, Molecular Medicine, UMass Medical School Craig Ceol, Molecular Medicine, UMass Medical School 1 0.90948   0.15   0.81986   0.58797   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-12-03 Adult Adult Skin Surface Structure
67332 67332 SRR17117614 SRX13302161 SRS11213386 SRP349128 PRJNA785890 Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish GSE190115 Transcriptome Analysis To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration   pubmed:37021774   WT Day1 GSM5714329   tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:1 WT Day1 Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects Tgmitfa:nlsEGFP FACS enriched cells 750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age genotype:WT|day:1 GSM5714329 GSM5714329: WT Day1; Danio rerio; RNA Seq GSM5714329 r1 GSM5714329 1 Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP349128   assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate WTD1_possorted_genome_bam.bam 10X Genomics bam file 11285903150.0 225718063.0 GSM5714329 r1 0:50 A:3319310923;C:2416106902;G:2709775130;T:2835193792;N:5516403 50       3319310923 2416106902 2709775130 2835193792 5516403 SRX13302161 SRS11213386 SRA1620868 Craig Ceol, Molecular Medicine, UMass Medical School Craig Ceol, Molecular Medicine, UMass Medical School 1 0.90815   0.15237   0.82181   0.57459   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-12-03 Adult Adult Skin Surface Structure
67333 67333 SRR17117615 SRX13302160 SRS11213385 SRP349128 PRJNA785890 Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish GSE190115 Transcriptome Analysis To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration   pubmed:37021774   WT day x 2 GSM5714328   tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:0 WT day x 2 Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects Tgmitfa:nlsEGFP FACS enriched cells 750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age genotype:WT|day:0 GSM5714328 GSM5714328: WT day x 2; Danio rerio; RNA Seq GSM5714328 r1 GSM5714328 1 Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP349128   assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate WTD0B_possorted_genome_bam.bam 10X Genomics bam file 6680383400.0 133607668.0 GSM5714328 r1 0:50 A:2032360836;C:1342388936;G:1478261391;T:1825537806;N:1834431 50       2032360836 1342388936 1478261391 1825537806 1834431 SRX13302160 SRS11213385 SRA1620868 Craig Ceol, Molecular Medicine, UMass Medical School Craig Ceol, Molecular Medicine, UMass Medical School 1 0.90381   0.1609   0.81813   0.61231   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-12-03 Adult Adult Skin Surface Structure
67334 67334 SRR17117616 SRX13302159 SRS11213384 SRP349128 PRJNA785890 Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish GSE190115 Transcriptome Analysis To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration   pubmed:37021774   WT day x 1 GSM5714327   tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:0 WT day x 1 Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects Tgmitfa:nlsEGFP FACS enriched cells 750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age genotype:WT|day:0 GSM5714327 GSM5714327: WT day x 1; Danio rerio; RNA Seq GSM5714327 r1 GSM5714327 1 Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP349128   assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate WTD0A_possorted_genome_bam.bam 10X Genomics bam file 7628491300.0 152569826.0 GSM5714327 r1 0:50 A:2377995758;C:1521202402;G:1696947530;T:2030231260;N:2114350 50       2377995758 1521202402 1696947530 2030231260 2114350 SRX13302159 SRS11213384 SRA1620868 Craig Ceol, Molecular Medicine, UMass Medical School Craig Ceol, Molecular Medicine, UMass Medical School 1 0.90188   0.1668   0.82154   0.599   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-12-03 Adult Adult Skin Surface Structure

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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");;