{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", technology = \"10x\" and tissue_curation = \"Trunk\"", "rows": [[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.", null, "pubmed:29644996", null, "Larva F1 2 scar", "GSM3032175", null, "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 times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with CIGAR  cell name  cell barcode and UMI sequence.", "Full organism", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM3032175", "GSM3032175: Larva F1 2 scar; Danio rerio; OTHER", "GSM3032175", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032175", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, null, 2682085389, 3008788535, 2093169318, 1516220703, 1664627, "SRX3768872", "SRS3023386", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "Germany", "2018-03-06", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Larva F1 1 scar", "GSM3032174", null, "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 times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with CIGAR  cell name  cell barcode and UMI sequence.", "Full organism", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM3032174", "GSM3032174: Larva F1 1 scar; Danio rerio; OTHER", "GSM3032174", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032174", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, null, 2222016153, 2555237987, 1722216404, 1271855931, 1387101, "SRX3768871", "SRS3023388", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "Germany", "2018-03-06", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Larva F1 2 mRNA", "GSM3032173", null, "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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM3032173", "GSM3032173: Larva F1 2 mRNA; Danio rerio; RNA Seq", "GSM3032173", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032173", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, null, 8264355452, 6830431714, 7093261338, 7804053400, 5378804, "SRX3768870", "SRS3023387", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "Germany", "2018-03-06", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Larva F1 1 mRNA", "GSM3032172", null, "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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM3032172", "GSM3032172: Larva F1 1 mRNA; Danio rerio; RNA Seq", "GSM3032172", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032172", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, null, 7365353958, 6068313931, 6251004125, 6996410946, 4793112, "SRX3768869", "SRS3023385", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "Germany", "2018-03-06", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Larva 5 scar", "GSM3032167", null, "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 times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.", "Full organism", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM3032167", "GSM3032167: Larva 5 scar; Danio rerio; OTHER", "GSM3032167", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032167", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, null, 2173948352, 2439410929, 1714624642, 1343296377, 1365400, "SRX3768864", "SRS3023381", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "Germany", "2018-03-06", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Larva 4 scar", "GSM3032166", null, "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 times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.", "Full organism", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM3032166", "GSM3032166: Larva 4 scar; Danio rerio; OTHER", "GSM3032166", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032166", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, null, 2080254513, 2296727471, 1625115068, 1232786300, 1300452, "SRX3768863", "SRS3023380", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "Germany", "2018-03-06", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Larva 5 mRNA", "GSM3032161", null, "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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM3032161", "GSM3032161: Larva 5 mRNA; Danio rerio; RNA Seq", "GSM3032161", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032161", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, null, 7637677199, 6210942203, 6438364980, 7117667800, 4904630, "SRX3768858", "SRS3023376", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "Germany", "2018-03-06", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Larva 4 mRNA", "GSM3032160", null, "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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM3032160", "GSM3032160: Larva 4 mRNA; Danio rerio; RNA Seq", "GSM3032160", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032160", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, null, 5483727144, 4548396363, 4737957565, 5002119078, 3511306, "SRX3768857", "SRS3023374", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "Germany", "2018-03-06", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Larva 3 mRNA", "GSM3032159", null, "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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM3032159", "GSM3032159: Larva 3 mRNA; Danio rerio; RNA Seq", "GSM3032159", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032159", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, 2047850756, 1318672327, 1403772432, 1743394108, 52287, "SRX3768856", "SRS3023373", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 1, 0.87661, null, 0.06466, null, 0.86614, null, 0.53364, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2018-03-06", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Larva 2 mRNA", "GSM2830057", null, "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 Gr\u00fcn 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 \u2013 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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM2830057", "GSM2830057: Larva 2 mRNA; Danio rerio; RNA Seq", "GSM2830057", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM2830057", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, 6582076349, 4985163175, 5131319282, 6085835988, 3297756, "SRX3320762", "SRS2626335", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 1, 0.9378, null, 0.05825, null, 0.79687, null, 0.50342, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2017-10-24", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Larva 1 mRNA", "GSM2830056", null, "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 Gr\u00fcn 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 \u2013 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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM2830056", "GSM2830056: Larva 1 mRNA; Danio rerio; RNA Seq", "GSM2830056", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM2830056", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, 9121762570, 5889322717, 6251660049, 8039869338, 228116, "SRX3320760", "SRS2626333", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 1, 0.88569, null, 0.08353, null, 0.86016, null, 0.53379, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2017-10-24", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Larva 1 mRNA", "GSM2830056", null, "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 Gr\u00fcn 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 \u2013 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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM2830056", "GSM2830056: Larva 1 mRNA; Danio rerio; RNA Seq", "GSM2830056", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM2830056", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, 1890861891, 1307860042, 1403340071, 1654667424, 45902, "SRX3320760", "SRS2626333", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 1, 0.89198, null, 0.07477, null, 0.87288, null, 0.49519, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2017-10-24", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Larva 1 scar", "GSM2830049", null, "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 times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. In the fourth filtering step  we determined the distribution of reads for the scars we had kept so far. Based on this distribution  we set a cut off and filtered out the scars that did not have at least this number of reads. Finally  for each cell type  we determined the distribution of different scars seen per cell and set a maximum number of scars a cell of that type can have. We filtered out cells in which we observed more than this maximum number as possible doublets. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.", "Full organism", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM2830049", "GSM2830049: Larva 1 scar; Danio rerio; OTHER", "GSM2830049", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM2830049", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, 286107087, 390283378, 268551180, 159171790, 5555, "SRX3320753", "SRS2626327", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 1, 0.00515, null, 8e-05, null, 0.99959, null, 0.24561, null, 130, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2017-10-24", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Larva 1 scar", "GSM2830049", null, "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 times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. In the fourth filtering step  we determined the distribution of reads for the scars we had kept so far. Based on this distribution  we set a cut off and filtered out the scars that did not have at least this number of reads. Finally  for each cell type  we determined the distribution of different scars seen per cell and set a maximum number of scars a cell of that type can have. We filtered out cells in which we observed more than this maximum number as possible doublets. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.", "Full organism", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM2830049", "GSM2830049: Larva 1 scar; Danio rerio; OTHER", "GSM2830049", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM2830049", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, 232542409, 315925727, 218437491, 129610895, 4168, "SRX3320753", "SRS2626327", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 1, 0.00786, null, 0.0, null, 0.99922, null, 0.31764, null, 130, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2017-10-24", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:31140974;pubmed:33933422", null, "Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 7", "GSM3764578", null, "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 \u00b0C 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", null, "1", "10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP198298", null, "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, null, null, null, 1897524564, 1180297377, 1360942367, 1732425907, 3368643, "SRX5827022", "SRS4754836", "SRA886020", "GEO", "Biology, University of Virginia", 1, 0.91289, null, 0.25388, null, 0.82856, null, 0.50847, null, 57, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-05-13", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:31140974;pubmed:33933422", null, "Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 6", "GSM3764577", null, "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 \u00b0C 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", null, "1", "10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP198298", null, "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, null, null, null, 1320513576, 874241368, 1044266437, 1169033783, 2222423, "SRX5827021", "SRS4754835", "SRA886020", "GEO", "Biology, University of Virginia", 1, 0.92536, null, 0.20155, null, 0.83473, null, 0.50983, null, 57, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-05-13", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:31140974;pubmed:33933422", null, "Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 5", "GSM3764576", null, "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 \u00b0C 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", null, "1", "10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP198298", null, "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, null, null, null, 2380116568, 1626615273, 2248860789, 2185343861, 3296247, "SRX5827020", "SRS4754834", "SRA886020", "GEO", "Biology, University of Virginia", 1, 0.91177, null, 0.16393, null, 0.80509, null, 0.514, null, 57, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-05-13", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:31140974;pubmed:33933422", null, "Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 4", "GSM3764575", null, "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 \u00b0C 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", null, "1", "10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP198298", null, "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, null, null, null, 2469579044, 1654897730, 2303443265, 2280478208, 3403207, "SRX5827019", "SRS4754833", "SRA886020", "GEO", "Biology, University of Virginia", 1, 0.90749, null, 0.17908, null, 0.8017, null, 0.5124, null, 57, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-05-13", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:31140974;pubmed:33933422", null, "Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 3", "GSM3764574", null, "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 \u00b0C 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", null, "1", "10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP198298", null, "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, null, null, null, 4458931221, 3243678800, 3916155957, 3908839406, 3221381, "SRX5827018", "SRS4754832", "SRA886020", "GEO", "Biology, University of Virginia", 1, 0.94166, null, 0.13327, null, 0.79304, null, 0.49472, null, 57, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-05-13", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:31140974;pubmed:33933422", null, "Neural crest derived cells from hypothyroid  juvenile zebrafish trunks  biological replicate 1", "GSM3764572", null, "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 \u00b0C 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", null, "1", "10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP198298", null, "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, null, null, null, 1526791201, 989860604, 1192544480, 1366270035, 2704663, "SRX5827016", "SRS4754830", "SRA886020", "GEO", "Biology, University of Virginia", 1, 0.92899, null, 0.25348, null, 0.83571, null, 0.48794, null, 57, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-05-13", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [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.", null, "pubmed:31140974;pubmed:33933422", null, "Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 6", "GSM3764571", null, "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 \u00b0C 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", null, "1", "10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP198298", null, "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, null, null, null, 1638197208, 1052881199, 1241396499, 1476057783, 2883835, "SRX5827015", "SRS4754829", "SRA886020", "GEO", "Biology, University of Virginia", 1, 0.91678, null, 0.23274, null, 0.83435, null, 0.51765, null, 57, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-05-13", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:31140974;pubmed:33933422", null, "Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 5", "GSM3764570", null, "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 \u00b0C 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", null, "1", "10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP198298", null, "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, null, null, null, 2330538697, 1602893033, 2265568086, 2124697512, 3276777, "SRX5827014", "SRS4754828", "SRA886020", "GEO", "Biology, University of Virginia", 1, 0.91032, null, 0.14841, null, 0.81207, null, 0.52798, null, 57, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-05-13", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:31140974;pubmed:33933422", null, "Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 4", "GSM3764569", null, "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 \u00b0C 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", null, "1", "10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP198298", null, "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, null, null, null, 2659154932, 1836434156, 2596847773, 2428811653, 3737227, "SRX5827013", "SRS4754827", "SRA886020", "GEO", "Biology, University of Virginia", 1, 0.91042, null, 0.14492, null, 0.81148, null, 0.53287, null, 57, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-05-13", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:31140974;pubmed:33933422", null, "Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 3", "GSM3764568", null, "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 \u00b0C 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", null, "1", "10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP198298", null, "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, null, null, null, 4144426475, 3024945467, 3685756189, 3690427238, 3013937, "SRX5827012", "SRS4754826", "SRA886020", "GEO", "Biology, University of Virginia", 1, 0.94033, null, 0.12393, null, 0.79338, null, 0.50069, null, 57, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-05-13", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:31140974;pubmed:33933422", null, "Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 1", "GSM3764566", null, "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 \u00b0C 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", null, "1", "10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP198298", null, "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, null, null, null, 1531421605, 966957285, 1151579626, 1352667292, 2608146, "SRX5827010", "SRS4754824", "SRA886020", "GEO", "Biology, University of Virginia", 1, 0.92288, null, 0.25231, null, 0.83479, null, 0.5014, null, 57, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-05-13", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [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.", null, "pubmed:34234366", null, "Zf 30h trunk", "GSM4631066", null, "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", null, "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", null, "age:30 hpf|tissue:trunk|genotype:wildtype", "GSM4631066", "GSM4631066: Zf 30h trunk; Danio rerio; RNA Seq", "GSM4631066", null, "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", null, "SRP268312", null, "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, null, 8739694698, 6736998816, 6903125001, 8168427703, 20277404, "SRX8595501", "SRS6886082", "SRA1089692", "GEO", "University of South Florida", 1, 0.88066, null, 0.09296, null, 0.8506, null, 0.50586, null, 147, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "10x", null, "United States", "2020-06-22", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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.", null, "pubmed:34234366", null, "Zf 30h trunk", "GSM4631066", null, "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", null, "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", null, "age:30 hpf|tissue:trunk|genotype:wildtype", "GSM4631066", "GSM4631066: Zf 30h trunk; Danio rerio; RNA Seq", "GSM4631066", null, "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", null, "SRP268312", null, "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, null, 8978925123, 6926043302, 7091713953, 8399543364, 32147234, "SRX8595501", "SRS6886082", "SRA1089692", "GEO", "University of South Florida", 1, 0.87666, null, 0.09235, null, 0.85277, null, 0.49776, null, 147, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "10x", null, "United States", "2020-06-22", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:36063998", null, "olig2+ cells in zebrafish trunks", "GSM5406686", null, "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 \u201cexpressed\u201d. 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", null, "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\u2019 Library and Gel Bead kit V3", null, "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", null, "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", null, "SRP325962", null, null, "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, null, null, 6848745621, 5731974961, 10959380121, 7859959179, 352118, "SRX11248236", "SRS9294118", "SRA1251944", "GEO", "Nantong University", 2, 0.0, 0.89636, 0.0, 0.20375, 1.0, 0.78575, null, 0.50155, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-06-29", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:36063998", null, "olig2+ cells in zebrafish trunks", "GSM5406686", null, "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 \u201cexpressed\u201d. 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", null, "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\u2019 Library and Gel Bead kit V3", null, "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", null, "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", null, "SRP325962", null, null, "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, null, null, 5431710090, 4568888734, 8717963207, 6239757593, 280876, "SRX11248236", "SRS9294118", "SRA1251944", "GEO", "Nantong University", 2, 0.0, 0.89635, 0.0, 0.20299, 1.0, 0.78453, null, 0.50241, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-06-29", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:36063998", null, "olig2+ cells in zebrafish trunks", "GSM5406686", null, "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 \u201cexpressed\u201d. 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", null, "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\u2019 Library and Gel Bead kit V3", null, "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", null, "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", null, "SRP325962", null, null, "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, null, null, 4513259900, 3774781009, 7221748955, 5183345869, 232767, "SRX11248236", "SRS9294118", "SRA1251944", "GEO", "Nantong University", 2, 0.0, 0.89637, 0.0, 0.20432, 1.0, 0.78439, null, 0.4973, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-06-29", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:36063998", null, "olig2+ cells in zebrafish trunks", "GSM5406686", null, "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 \u201cexpressed\u201d. 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", null, "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\u2019 Library and Gel Bead kit V3", null, "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", null, "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", null, "SRP325962", null, null, "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, null, null, 4874539429, 4084280591, 7793747016, 5594741104, 249560, "SRX11248236", "SRS9294118", "SRA1251944", "GEO", "Nantong University", 2, 0.0, 0.89737, 0.0, 0.20476, 1.0, 0.78675, null, 0.5017, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-06-29", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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  taking note of their sample origin.", null, "pubmed:35355015", null, "XBN", "GSM5510265", null, "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", null, "Droplet based scRNA seq was performed using the Chromium Single Cell 3\u2019 Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3\u2019 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", null, "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", null, "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", null, "SRP331755", null, null, "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, null, null, 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", null, "United States", "2021-08-09", "Undetermined", "Adult", "Trunk", "Surface Structure"], [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  taking note of their sample origin.", null, "pubmed:35355015", null, "XBN", "GSM5510265", null, "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", null, "Droplet based scRNA seq was performed using the Chromium Single Cell 3\u2019 Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3\u2019 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", null, "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", null, "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", null, "SRP331755", null, null, "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, null, null, 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", null, "United States", "2021-08-09", "Undetermined", "Adult", "Trunk", "Surface Structure"], [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  taking note of their sample origin.", null, "pubmed:35355015", null, "XBG", "GSM5510264", null, "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", null, "Droplet based scRNA seq was performed using the Chromium Single Cell 3\u2019 Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3\u2019 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", null, "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", null, "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", null, "SRP331755", null, null, "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, null, null, 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", null, "United States", "2021-08-09", "Undetermined", "Adult", "Trunk", "Surface Structure"], [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  taking note of their sample origin.", null, "pubmed:35355015", null, "XBG", "GSM5510264", null, "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", null, "Droplet based scRNA seq was performed using the Chromium Single Cell 3\u2019 Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3\u2019 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", null, "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", null, "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", null, "SRP331755", null, null, "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, null, null, 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", null, "United States", "2021-08-09", "Undetermined", "Adult", "Trunk", "Surface Structure"], [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", null, "pubmed:36063998", null, "olig2+ cells in zebrafish trunks   60hpf", "GSM5639644", null, "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 \u201cexpressed\u201d. 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", null, "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\u2019 Library and Gel Bead kit V3", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342165", null, null, "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, null, null, 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, null, 0.51047, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-10-19", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:36063998", null, "olig2+ cells in zebrafish trunks   60hpf", "GSM5639644", null, "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 \u201cexpressed\u201d. 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", null, "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\u2019 Library and Gel Bead kit V3", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342165", null, null, "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, null, null, 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, null, 0.50682, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-10-19", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:36063998", null, "olig2+ cells in zebrafish trunks   60hpf", "GSM5639644", null, "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 \u201cexpressed\u201d. 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", null, "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\u2019 Library and Gel Bead kit V3", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342165", null, null, "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, null, null, 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, null, 0.50544, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-10-19", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:36063998", null, "olig2+ cells in zebrafish trunks   60hpf", "GSM5639644", null, "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 \u201cexpressed\u201d. 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", null, "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\u2019 Library and Gel Bead kit V3", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342165", null, null, "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, null, null, 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, null, 0.51059, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-10-19", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:36063998", null, "olig2+ cells in zebrafish trunks   28hpf", "GSM5639643", null, "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 \u201cexpressed\u201d. 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", null, "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\u2019 Library and Gel Bead kit V3", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342165", null, null, "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, null, null, 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, null, 0.49581, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-10-19", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:36063998", null, "olig2+ cells in zebrafish trunks   28hpf", "GSM5639643", null, "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 \u201cexpressed\u201d. 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", null, "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\u2019 Library and Gel Bead kit V3", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342165", null, null, "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, null, null, 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, null, 0.50368, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-10-19", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:36063998", null, "olig2+ cells in zebrafish trunks   28hpf", "GSM5639643", null, "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 \u201cexpressed\u201d. 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", null, "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\u2019 Library and Gel Bead kit V3", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342165", null, null, "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, null, null, 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, null, 0.50003, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-10-19", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:36063998", null, "olig2+ cells in zebrafish trunks   28hpf", "GSM5639643", null, "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 \u201cexpressed\u201d. 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", null, "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\u2019 Library and Gel Bead kit V3", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342165", null, null, "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, null, null, 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, null, 0.4925, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-10-19", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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", null, "DP1 36hpf", "GSM7083138", null, "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\uff0craw 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\u00a0\u2265 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", null, "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\u2019 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\u2019 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 Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.", null, "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 prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342737", null, null, "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, null, null, 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", null, "China", "2023-03-06", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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", null, "DP2 36hpf", "GSM7083139", null, "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\uff0craw 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\u00a0\u2265 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", null, "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\u2019 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\u2019 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 Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.", null, "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 prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342737", null, null, "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, null, null, 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", null, "China", "2023-03-06", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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", null, "SP 36hpf", "GSM7083140", null, "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\uff0craw 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\u00a0\u2265 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", null, "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\u2019 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\u2019 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 Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.", null, "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 prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342737", null, null, "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, null, null, 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", null, "China", "2023-03-06", "Pharyngula", "Embryo", "Trunk", "Surface Structure"]], "truncated": false, "filtered_table_rows_count": 46, "expanded_columns": [], "expandable_columns": [], "columns": ["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", 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