{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"cDNA\", technology = \"10x\" and tissue_curation = \"Fin\"", "rows": [[29197, "SRR27321690", "SRX22998813", "SRS19963383", "SRP479569", "PRJNA1055522", "Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin", "GSE251828", "Transcriptome Analysis", "This study investigated the cell composition and lineage relationships of FACS fluorescence activated cell sorting enriched epidermal  bone forming osteoblast and non osteoblast blastemal fin regenerate cells by single cell sc RNA sequencing. The repetitive cell harvesting in four week intervals revealed a constant gene regulation over four successive regeneration rounds in the early outgrowth stage. In addition  the sc RNA dataset uncovered a potential lineage relationship between distal blastema cells and osteoblasts during fin regeneration. These findings  together with the identification of novel fin regenerate markers  advance our understanding of complex tissue regeneration in zebrafish. Overall design: To study potentially underrepresented cell populations during zebrafish fin regeneration  we harvested single cells and FACS enriched for siam+  shha+  osterix+  RUNX2+ cells via respective mCherry and GFP reporter fluorophores. We performed gene expression analysis using data obtained from RNA seq of enriched cells from 4 successive regeneration stages at 3 dpa.", null, "pubmed:38318374", null, "4th round of regeneration", "GSM7988809", null, "source name:Fin|tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation|geo loc name:missing|collection date:missing", "4th round of regeneration", "A reference based on GRCz10  Ensembl annotation e98 was created  by first adding the sequences of gfp and mCherry as separate chromosomes to the fa file and the gtf file and then building the cellranger reference using cellranger mkref v3.0.0 fastq files were processed with `cellranger count` from 10X genomics version 3.0.0 Assembly: GRCz10 Supplementary files format and content: HDF5 Feature Barcode Matrix Format.", "Fin", "Fin regenerates of quadruple transgenic fish [Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259] were harvested at 3 dpa  cut into small pieces with a scalpel and transferred into 1 ml collagenase dispase solution 1 mg/ml in PBS  Roche #10269638001 for 10 min at 28\u00b0C. The sample was pipetted slowly up and down with an elongated  flame polished Pasteur pipette. The procedure was repeated 4 times with decreasing inner tip diameters of the Pasteur pipettes until a homogenous solution was obtained. The dissociates were poured onto an equilibrated 70 \u00b5m cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2  Gibco #12082739. post centrifugation 15 minutes  1800 rpm  4\u00b0C  the supernatant was discarded and the remaining cell pellet resuspended in 500 \u00b5l 2% BSA in PBS. Calcein violet 1\u00b5l 10mM  Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet  GFP and mCherry+ cells were collected in 50 \u00b5l 2% BSA in PBS via fluorescence activated cell sorting BD LSR Fortessa and processed for single cell RNA sequencing analysis based on 10X Genomics 10X Chromium system  10X library preparation according to the manufacturer's instructions.", "For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 \u00b5l of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell 3\u2019 RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer\u2019s guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.", null, "tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation", "GSM7988809", "GSM7988809: 4th round of regeneration; Danio rerio; RNA Seq", "GSM7988809 r1", "GSM7988809", "1", "For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 \u00b5l of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell three prime RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer's guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP479569", null, null, "L33268_osteoblasts_reg4_R2.fastq.gz L33268_osteoblasts_reg4_R1.fastq.gz", "fastq fastq", 7429523805.0, 89512335.0, "GSM7988809 r1", "0:26 1:57", "A:2056160949;C:1638835280;G:1683264344;T:2047119393;N:4143839", 26, 57, null, null, 2056160949, 1638835280, 1683264344, 2047119393, 4143839, "SRX22998813", "SRS19963383", "SRA1774238", "Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden", "Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden", 2, 0.00833, 0.93478, 0.00199, 0.12451, 0.9849, 0.82418, 0.46227, 0.53386, 26, 57, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-12-21", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [29198, "SRR27321691", "SRX22998812", "SRS19963382", "SRP479569", "PRJNA1055522", "Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin", "GSE251828", "Transcriptome Analysis", "This study investigated the cell composition and lineage relationships of FACS fluorescence activated cell sorting enriched epidermal  bone forming osteoblast and non osteoblast blastemal fin regenerate cells by single cell sc RNA sequencing. The repetitive cell harvesting in four week intervals revealed a constant gene regulation over four successive regeneration rounds in the early outgrowth stage. In addition  the sc RNA dataset uncovered a potential lineage relationship between distal blastema cells and osteoblasts during fin regeneration. These findings  together with the identification of novel fin regenerate markers  advance our understanding of complex tissue regeneration in zebrafish. Overall design: To study potentially underrepresented cell populations during zebrafish fin regeneration  we harvested single cells and FACS enriched for siam+  shha+  osterix+  RUNX2+ cells via respective mCherry and GFP reporter fluorophores. We performed gene expression analysis using data obtained from RNA seq of enriched cells from 4 successive regeneration stages at 3 dpa.", null, "pubmed:38318374", null, "3rd round of regeneration", "GSM7988808", null, "source name:Fin|tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation|geo loc name:missing|collection date:missing", "3rd round of regeneration", "A reference based on GRCz10  Ensembl annotation e98 was created  by first adding the sequences of gfp and mCherry as separate chromosomes to the fa file and the gtf file and then building the cellranger reference using cellranger mkref v3.0.0 fastq files were processed with `cellranger count` from 10X genomics version 3.0.0 Assembly: GRCz10 Supplementary files format and content: HDF5 Feature Barcode Matrix Format.", "Fin", "Fin regenerates of quadruple transgenic fish [Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259] were harvested at 3 dpa  cut into small pieces with a scalpel and transferred into 1 ml collagenase dispase solution 1 mg/ml in PBS  Roche #10269638001 for 10 min at 28\u00b0C. The sample was pipetted slowly up and down with an elongated  flame polished Pasteur pipette. The procedure was repeated 4 times with decreasing inner tip diameters of the Pasteur pipettes until a homogenous solution was obtained. The dissociates were poured onto an equilibrated 70 \u00b5m cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2  Gibco #12082739. post centrifugation 15 minutes  1800 rpm  4\u00b0C  the supernatant was discarded and the remaining cell pellet resuspended in 500 \u00b5l 2% BSA in PBS. Calcein violet 1\u00b5l 10mM  Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet  GFP and mCherry+ cells were collected in 50 \u00b5l 2% BSA in PBS via fluorescence activated cell sorting BD LSR Fortessa and processed for single cell RNA sequencing analysis based on 10X Genomics 10X Chromium system  10X library preparation according to the manufacturer's instructions.", "For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 \u00b5l of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell 3\u2019 RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer\u2019s guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.", null, "tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation", "GSM7988808", "GSM7988808: 3rd round of regeneration; Danio rerio; RNA Seq", "GSM7988808 r1", "GSM7988808", "1", "For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 \u00b5l of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell three prime RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer's guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP479569", null, null, "L33267_osteoblasts_reg3_R1.fastq.gz L33267_osteoblasts_reg3_R2.fastq.gz", "fastq fastq", 5171923722.0, 62312334.0, "GSM7988808 r1", "0:26 1:57", "A:1429339406;C:1125953827;G:1205184308;T:1408611366;N:2834815", 26, 57, null, null, 1429339406, 1125953827, 1205184308, 1408611366, 2834815, "SRX22998812", "SRS19963382", "SRA1774238", "Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden", "Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden", 2, 0.01041, 0.92057, 0.00236, 0.13516, 0.98198, 0.82244, 0.45267, 0.53338, 26, 57, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-12-21", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [29199, "SRR27321692", "SRX22998811", "SRS19963381", "SRP479569", "PRJNA1055522", "Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin", "GSE251828", "Transcriptome Analysis", "This study investigated the cell composition and lineage relationships of FACS fluorescence activated cell sorting enriched epidermal  bone forming osteoblast and non osteoblast blastemal fin regenerate cells by single cell sc RNA sequencing. The repetitive cell harvesting in four week intervals revealed a constant gene regulation over four successive regeneration rounds in the early outgrowth stage. In addition  the sc RNA dataset uncovered a potential lineage relationship between distal blastema cells and osteoblasts during fin regeneration. These findings  together with the identification of novel fin regenerate markers  advance our understanding of complex tissue regeneration in zebrafish. Overall design: To study potentially underrepresented cell populations during zebrafish fin regeneration  we harvested single cells and FACS enriched for siam+  shha+  osterix+  RUNX2+ cells via respective mCherry and GFP reporter fluorophores. We performed gene expression analysis using data obtained from RNA seq of enriched cells from 4 successive regeneration stages at 3 dpa.", null, "pubmed:38318374", null, "2nd round of regeneration", "GSM7988807", null, "source name:Fin|tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation|geo loc name:missing|collection date:missing", "2nd round of regeneration", "A reference based on GRCz10  Ensembl annotation e98 was created  by first adding the sequences of gfp and mCherry as separate chromosomes to the fa file and the gtf file and then building the cellranger reference using cellranger mkref v3.0.0 fastq files were processed with `cellranger count` from 10X genomics version 3.0.0 Assembly: GRCz10 Supplementary files format and content: HDF5 Feature Barcode Matrix Format.", "Fin", "Fin regenerates of quadruple transgenic fish [Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259] were harvested at 3 dpa  cut into small pieces with a scalpel and transferred into 1 ml collagenase dispase solution 1 mg/ml in PBS  Roche #10269638001 for 10 min at 28\u00b0C. The sample was pipetted slowly up and down with an elongated  flame polished Pasteur pipette. The procedure was repeated 4 times with decreasing inner tip diameters of the Pasteur pipettes until a homogenous solution was obtained. The dissociates were poured onto an equilibrated 70 \u00b5m cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2  Gibco #12082739. post centrifugation 15 minutes  1800 rpm  4\u00b0C  the supernatant was discarded and the remaining cell pellet resuspended in 500 \u00b5l 2% BSA in PBS. Calcein violet 1\u00b5l 10mM  Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet  GFP and mCherry+ cells were collected in 50 \u00b5l 2% BSA in PBS via fluorescence activated cell sorting BD LSR Fortessa and processed for single cell RNA sequencing analysis based on 10X Genomics 10X Chromium system  10X library preparation according to the manufacturer's instructions.", "For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 \u00b5l of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell 3\u2019 RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer\u2019s guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.", null, "tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation", "GSM7988807", "GSM7988807: 2nd round of regeneration; Danio rerio; RNA Seq", "GSM7988807 r1", "GSM7988807", "1", "For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 \u00b5l of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell three prime RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer's guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP479569", null, null, "L32508_osteoblasts_reg2_R1.fastq.gz L32508_osteoblasts_reg2_R2.fastq.gz", "fastq fastq", 6922720659.0, 83406273.0, "GSM7988807 r1", "0:26 1:57", "A:1901173243;C:1540845413;G:1598673449;T:1877295749;N:4732805", 26, 57, null, null, 1901173243, 1540845413, 1598673449, 1877295749, 4732805, "SRX22998811", "SRS19963381", "SRA1774238", "Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden", "Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden", 2, 0.00257, 0.93924, 0.00083, 0.10412, 0.99474, 0.83023, 0.47435, 0.51839, 26, 57, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-12-21", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [29200, "SRR27321693", "SRX22998810", "SRS19963380", "SRP479569", "PRJNA1055522", "Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin", "GSE251828", "Transcriptome Analysis", "This study investigated the cell composition and lineage relationships of FACS fluorescence activated cell sorting enriched epidermal  bone forming osteoblast and non osteoblast blastemal fin regenerate cells by single cell sc RNA sequencing. The repetitive cell harvesting in four week intervals revealed a constant gene regulation over four successive regeneration rounds in the early outgrowth stage. In addition  the sc RNA dataset uncovered a potential lineage relationship between distal blastema cells and osteoblasts during fin regeneration. These findings  together with the identification of novel fin regenerate markers  advance our understanding of complex tissue regeneration in zebrafish. Overall design: To study potentially underrepresented cell populations during zebrafish fin regeneration  we harvested single cells and FACS enriched for siam+  shha+  osterix+  RUNX2+ cells via respective mCherry and GFP reporter fluorophores. We performed gene expression analysis using data obtained from RNA seq of enriched cells from 4 successive regeneration stages at 3 dpa.", null, "pubmed:38318374", null, "1st round of regeneration", "GSM7988806", null, "source name:Fin|tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation|geo loc name:missing|collection date:missing", "1st round of regeneration", "A reference based on GRCz10  Ensembl annotation e98 was created  by first adding the sequences of gfp and mCherry as separate chromosomes to the fa file and the gtf file and then building the cellranger reference using cellranger mkref v3.0.0 fastq files were processed with `cellranger count` from 10X genomics version 3.0.0 Assembly: GRCz10 Supplementary files format and content: HDF5 Feature Barcode Matrix Format.", "Fin", "Fin regenerates of quadruple transgenic fish [Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259] were harvested at 3 dpa  cut into small pieces with a scalpel and transferred into 1 ml collagenase dispase solution 1 mg/ml in PBS  Roche #10269638001 for 10 min at 28\u00b0C. The sample was pipetted slowly up and down with an elongated  flame polished Pasteur pipette. The procedure was repeated 4 times with decreasing inner tip diameters of the Pasteur pipettes until a homogenous solution was obtained. The dissociates were poured onto an equilibrated 70 \u00b5m cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2  Gibco #12082739. post centrifugation 15 minutes  1800 rpm  4\u00b0C  the supernatant was discarded and the remaining cell pellet resuspended in 500 \u00b5l 2% BSA in PBS. Calcein violet 1\u00b5l 10mM  Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet  GFP and mCherry+ cells were collected in 50 \u00b5l 2% BSA in PBS via fluorescence activated cell sorting BD LSR Fortessa and processed for single cell RNA sequencing analysis based on 10X Genomics 10X Chromium system  10X library preparation according to the manufacturer's instructions.", "For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 \u00b5l of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell 3\u2019 RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer\u2019s guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.", null, "tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation", "GSM7988806", "GSM7988806: 1st round of regeneration; Danio rerio; RNA Seq", "GSM7988806 r1", "GSM7988806", "1", "For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 \u00b5l of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell three prime RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer's guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP479569", null, null, "L32023_osteoblasts_reg1_R1.fastq.gz L32023_osteoblasts_reg1_R2.fastq.gz", "fastq fastq", 15070528207.0, 181572629.0, "GSM7988806 r1", "0:26 1:57", "A:4238593010;C:3314457079;G:3500292725;T:4013398538;N:3786855", 26, 57, null, null, 4238593010, 3314457079, 3500292725, 4013398538, 3786855, "SRX22998810", "SRS19963380", "SRA1774238", "Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden", "Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden", 2, 0.01031, 0.92947, 0.00392, 0.17331, 0.98526, 0.81815, 0.4321, 0.54688, 26, 57, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-12-21", "Undetermined", "Undetermined", "Fin", "Surface Structure"], [30628, "SRR27942672", "SRX23599456", "SRS20442304", "SRP489317", "PRJNA1075480", "Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution", "PRJNA1075480", "Other", "Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.", null, "pubmed:39809530", null, "6 day post amputation replicate 2", "6dpa fin2", null, "strain:Tgsp7:EGFP|age:1 year|collection date:2022 02 04|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:6 day post amputation replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "6dpa fin2 snRNA", "6dpa2 RNA", "6dpa2 RNA", "Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP489317", null, null, "6dpa2-GEX-lib1_S2_L001_R2_001.fastq.gz 6dpa2-GEX-lib1_S2_L001_R1_001.fastq.gz", "fastq fastq", 88818703262.0, 498981479.0, "6dpa2 GEX lib1 S2 L001 R1 001.fastq.gz", "0:28 1:150", "A:27051219358;C:18185699713;G:19496959258;T:24083822607;N:1002326", 28, 150, null, null, 27051219358, 18185699713, 19496959258, 24083822607, 1002326, "SRX23599456", "SRS20442304", "SRA1801018", "Washington University in St. Louis School of Medicine|Genetics", "Washington University in St. Louis School of Medicine", 2, 0.02864, 0.84751, 0.01449, 0.29092, 0.98169, 0.82014, 0.39586, 0.64356, 28, 150, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-12", "Adult", "Adult", "Fin", "Surface Structure"], [30629, "SRR27942673", "SRX23599455", "SRS20442303", "SRP489317", "PRJNA1075480", "Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution", "PRJNA1075480", "Other", "Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.", null, "pubmed:39809530", null, "6 day post amputation replicate 1", "6dpa fin1", null, "strain:Tgsp7:EGFP|age:1 year|collection date:2022 02 04|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:6 day post amputation replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "6dpa fin1 snRNA", "6dpa1 RNA", "6dpa1 RNA", "Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP489317", null, null, "6dpa1-GEX-lib1_S1_L001_R2_001.fastq.gz 6dpa1-GEX-lib1_S1_L001_R1_001.fastq.gz", "fastq fastq", 106483322870.0, 598220915.0, "6dpa1 GEX lib1 S1 L001 R1 001.fastq.gz", "0:28 1:150", "A:32833929738;C:22259209515;G:23233729505;T:28155235335;N:1218777", 28, 150, null, null, 32833929738, 22259209515, 23233729505, 28155235335, 1218777, "SRX23599455", "SRS20442303", "SRA1801018", "Washington University in St. Louis School of Medicine|Genetics", "Washington University in St. Louis School of Medicine", 2, 0.02691, 0.87324, 0.01263, 0.22013, 0.98415, 0.83144, 0.4808, 0.62463, 28, 150, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-12", "Adult", "Adult", "Fin", "Surface Structure"], [30630, "SRR27942674", "SRX23599454", "SRS20442302", "SRP489317", "PRJNA1075480", "Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution", "PRJNA1075480", "Other", "Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.", null, "pubmed:39809530", null, "4 day post amputation replicate 2", "4dpa fin2", null, "strain:Tgsp7:EGFP|age:1 year|collection date:2022 01 12|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:4 day post amputation replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "4dpa fin2 snRNA", "4dpa2 RNA", "4dpa2 RNA", "Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP489317", null, null, "4dpa2-GEX-lib1_S2_L002_R1_001.fastq.gz 4dpa2-GEX-lib1_S2_L002_R2_001.fastq.gz", "fastq fastq", 100355045420.0, 563792390.0, "4dpa2 GEX lib1 S2 L002 R1 001.fastq.gz", "0:28 1:150", "A:30110360316;C:21497825420;G:22061747902;T:26684746811;N:364971", 28, 150, null, null, 30110360316, 21497825420, 22061747902, 26684746811, 364971, "SRX23599454", "SRS20442302", "SRA1801018", "Washington University in St. Louis School of Medicine|Genetics", "Washington University in St. Louis School of Medicine", 2, 0.02956, 0.90492, 0.01391, 0.21143, 0.98324, 0.82347, 0.46993, 0.73177, 28, 150, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-12", "Adult", "Adult", "Fin", "Surface Structure"], [30631, "SRR27942675", "SRX23599453", "SRS20442301", "SRP489317", "PRJNA1075480", "Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution", "PRJNA1075480", "Other", "Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.", null, "pubmed:39809530", null, "4 day post amputation replicate 1", "4dpa fin1", null, "strain:Tgsp7:EGFP|age:1 year|collection date:2021 11 22|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:4 day post amputation replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "4dpa fin1 snRNA", "4dpa1 RNA", "4dpa1 RNA", "Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP489317", null, null, "4dpa1-GEX-lib1_S1_L002_R2_001.fastq.gz 4dpa1-GEX-lib1_S1_L002_R1_001.fastq.gz", "fastq fastq", 104945766346.0, 589582957.0, "4dpa1 GEX lib1 S1 L002 R1 001.fastq.gz", "0:28 1:150", "A:32489394291;C:21756067815;G:22868928766;T:27829952922;N:1422552", 28, 150, null, null, 32489394291, 21756067815, 22868928766, 27829952922, 1422552, "SRX23599453", "SRS20442301", "SRA1801018", "Washington University in St. Louis School of Medicine|Genetics", "Washington University in St. Louis School of Medicine", 2, 0.02921, 0.86985, 0.01399, 0.22211, 0.98372, 0.8294, 0.45783, 0.71655, 28, 150, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-12", "Adult", "Adult", "Fin", "Surface Structure"], [30632, "SRR27942676", "SRX23599452", "SRS20442300", "SRP489317", "PRJNA1075480", "Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution", "PRJNA1075480", "Other", "Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.", null, "pubmed:39809530", null, "2 day post amputation replicate 2", "2dpa fin2", null, "strain:Tgsp7:EGFP|age:1 year|collection date:2022 01 12|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:2 day post amputation replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "2dpa fin2 snRNA", "2dpa2 RNA", "2dpa2 RNA", "Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP489317", null, null, "2dpa2-GEX-lib1_S1_L001_R2_001.fastq.gz 2dpa2-GEX-lib1_S1_L001_R1_001.fastq.gz", "fastq fastq", 84977307334.0, 477400603.0, "2dpa2 GEX lib1 S1 L001 R1 001.fastq.gz", "0:28 1:150", "A:25498895454;C:18439149160;G:19015549944;T:22023275686;N:437090", 28, 150, null, null, 25498895454, 18439149160, 19015549944, 22023275686, 437090, "SRX23599452", "SRS20442300", "SRA1801018", "Washington University in St. Louis School of Medicine|Genetics", "Washington University in St. Louis School of Medicine", 2, 0.02811, 0.91493, 0.01297, 0.18571, 0.98492, 0.83554, 0.4671, 0.75085, 28, 150, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-12", "Adult", "Adult", "Fin", "Surface Structure"], [30633, "SRR27942677", "SRX23599451", "SRS20442299", "SRP489317", "PRJNA1075480", "Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution", "PRJNA1075480", "Other", "Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.", null, "pubmed:39809530", null, "2 day post amputation replicate 1", "2dpa fin1", null, "strain:Tgsp7:EGFP|age:1 year|collection date:2021 11 22|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:2 day post amputation replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "2dpa fin1 snRNA", "2dpa1 RNA", "2dpa1 RNA", "Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP489317", null, null, "2dpa1-GEX-lib1_S2_L002_R1_001.fastq.gz 2dpa1-GEX-lib1_S2_L002_R2_001.fastq.gz", "fastq fastq", 93046027220.0, 522730490.0, "2dpa1 GEX lib1 S2 L002 R1 001.fastq.gz", "0:28 1:150", "A:28562453325;C:19484276400;G:20294346104;T:24703683984;N:1267407", 28, 150, null, null, 28562453325, 19484276400, 20294346104, 24703683984, 1267407, "SRX23599451", "SRS20442299", "SRA1801018", "Washington University in St. Louis School of Medicine|Genetics", "Washington University in St. Louis School of Medicine", 2, 0.03074, 0.88234, 0.01398, 0.22441, 0.98405, 0.83268, 0.48065, 0.74026, 28, 150, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-12", "Adult", "Adult", "Fin", "Surface Structure"], [30634, "SRR27942678", "SRX23599450", "SRS20442298", "SRP489317", "PRJNA1075480", "Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution", "PRJNA1075480", "Other", "Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.", null, "pubmed:39809530", null, "1 day post amputation replicate 2", "1dpa fin2", null, "strain:Tgsp7:EGFP|age:1 year|collection date:2022 01 27|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:1 day post amputation replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "1dpa fin2 snRNA", "1dpa2 RNA", "1dpa2 RNA", "Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP489317", null, null, "1dpa2-GEX-lib1_S1_L004_R1_001.fastq.gz 1dpa2-GEX-lib1_S1_L004_R2_001.fastq.gz", "fastq fastq", 84562055050.0, 475067725.0, "1dpa2 GEX lib1 S1 L004 R1 001.fastq.gz", "0:28 1:150", "A:25830017026;C:17874013165;G:18722117096;T:22135719607;N:188156", 28, 150, null, null, 25830017026, 17874013165, 18722117096, 22135719607, 188156, "SRX23599450", "SRS20442298", "SRA1801018", "Washington University in St. Louis School of Medicine|Genetics", "Washington University in St. Louis School of Medicine", 2, 0.02723, 0.88745, 0.01218, 0.18561, 0.98573, 0.83613, 0.45958, 0.63016, 28, 150, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-12", "Adult", "Adult", "Fin", "Surface Structure"], [30635, "SRR27942679", "SRX23599449", "SRS20442297", "SRP489317", "PRJNA1075480", "Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution", "PRJNA1075480", "Other", "Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.", null, "pubmed:39809530", null, "1 day post amputation replicate 1", "1dpa fin1", null, "strain:Tgsp7:EGFP|age:1 year|collection date:2021 07 26|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:1 day post amputation replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "1dpa fin1 snRNA", "1dpa1 RNA", "1dpa1 RNA", "Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP489317", null, null, "1dpa1-GEX-lib1_S3_L002_R2_002.fastq.gz 1dpa1-GEX-lib1_S3_L002_R1_002.fastq.gz 1dpa1-GEX-lib1_S1_L001_R2_001.fastq.gz 1dpa1-GEX-lib1_S1_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 81494415866.0, 457833797.0, "1dpa1 GEX lib1 S1 L001 R1 001.fastq.gz", "0:28 1:150", "A:25109914971;C:16807439152;G:17406389176;T:22169842983;N:829584", 28, 150, null, null, 25109914971, 16807439152, 17406389176, 22169842983, 829584, "SRX23599449", "SRS20442297", "SRA1801018", "Washington University in St. Louis School of Medicine|Genetics", "Washington University in St. Louis School of Medicine", 2, 0.02792, 0.87908, 0.0123, 0.19441, 0.98194, 0.83644, 0.4621, 0.70445, 28, 150, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-12", "Adult", "Adult", "Fin", "Surface Structure"], [30636, "SRR27942690", "SRX23599438", "SRS20442296", "SRP489317", "PRJNA1075480", "Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution", "PRJNA1075480", "Other", "Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.", null, "pubmed:39809530", null, "0 day post amputation replicate 2", "0dpa fin2", null, "strain:Tgsp7:EGFP|age:1 year|collection date:2022 01 27|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:0 day post amputation replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "0dpa fin2 snRNA", "0dpa2 RNA", "0dpa2 RNA", "Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP489317", null, null, "0dpa2-GEX-lib1_S2_L004_R2_001.fastq.gz 0dpa2-GEX-lib1_S2_L004_R1_001.fastq.gz", "fastq fastq", 94016384252.0, 528181934.0, "0dpa2 GEX lib1 S2 L004 R1 001.fastq.gz", "0:28 1:150", "A:28851000041;C:19680536935;G:20640186670;T:24844451695;N:208911", 28, 150, null, null, 28851000041, 19680536935, 20640186670, 24844451695, 208911, "SRX23599438", "SRS20442296", "SRA1801018", "Washington University in St. Louis School of Medicine|Genetics", "Washington University in St. Louis School of Medicine", 2, 0.02684, 0.87686, 0.01274, 0.21544, 0.98703, 0.85975, 0.45722, 0.74164, 28, 150, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-12", "Adult", "Adult", "Fin", "Surface Structure"], [30637, "SRR27942691", "SRX23599437", "SRS20442295", "SRP489317", "PRJNA1075480", "Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution", "PRJNA1075480", "Other", "Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.", null, "pubmed:39809530", null, "0 day post amputation replicate 1", "0dpa fin1", null, "strain:Tgsp7:EGFP|age:1 year|collection date:2021 07 26|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:0 day post amputation replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "0dpa fin1 snRNA", "0dpa1 RNA", "0dpa1 RNA", "Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP489317", null, null, "0dpa1-GEX-lib1_S1_L001_R1_001.fastq.gz 0dpa1-GEX-lib1_S1_L001_R2_001.fastq.gz", "fastq fastq", 95106992388.0, 534308946.0, "0dpa1 GEX lib1 S1 L001 R1 001.fastq.gz", "0:28 1:150", "A:29570202174;C:19531427210;G:20167731244;T:25836092390;N:1539370", 28, 150, null, null, 29570202174, 19531427210, 20167731244, 25836092390, 1539370, "SRX23599437", "SRS20442295", "SRA1801018", "Washington University in St. Louis School of Medicine|Genetics", "Washington University in St. Louis School of Medicine", 2, 0.02388, 0.87039, 0.01162, 0.24031, 0.98652, 0.85354, 0.48963, 0.74378, 28, 150, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-02-12", "Adult", "Adult", "Fin", "Surface Structure"], [34143, "SRR31364121", "SRX26737888", "SRS23227909", "SRP545529", "PRJNA1186739", "Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish", "GSE282061", "Transcriptome Analysis", "The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  \u201cmelanoleucophores.\u201d To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.", null, "pubmed:40305763", null, "dataset3 BMPi LDN RFP", "GSM8635057", null, "source name:dorsal fin|tissue:dorsal fin|genotype:wild type|treatment:LDN|geo loc name:missing|collection date:missing", "dataset3 BMPi LDN RFP", "We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS", "dorsal fin", null, "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3\u2019 solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "tissue:dorsal fin|genotype:wild type|treatment:LDN", "GSM8635057", "GSM8635057: dataset3 BMPi LDN RFP; Danio rerio; RNA Seq", "GSM8635057 r1", "GSM8635057", "1", "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP545529", null, "loader:fastq load.py", "LDN_RFP_S4_L001_I1_001.fastq.gz LDN_RFP_S4_L001_I2_001.fastq.gz LDN_RFP_S4_L001_R1_001.fastq.gz LDN_RFP_S4_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 4755245952.0, 34458304.0, "GSM8635057 r1", "0:10 1:10 2:28 3:90", "A:926644119;C:661476939;G:733308280;T:779560094;N:257928", 10, 10, 28, 90, 926644119, 661476939, 733308280, 779560094, 257928, "SRX26737888", "SRS23227909", "SRA2016042", "UVA", "UVA", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Unknown", "2024-11-15", "Undetermined", "Embryo", "Fin", "Surface Structure"], [34144, "SRR31364122", "SRX26737887", "SRS23227908", "SRP545529", "PRJNA1186739", "Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish", "GSE282061", "Transcriptome Analysis", "The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  \u201cmelanoleucophores.\u201d To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.", null, "pubmed:40305763", null, "dataset3 BMPi LDN no RFP", "GSM8635056", null, "source name:dorsal fin|tissue:dorsal fin|genotype:wild type|treatment:LDN|geo loc name:missing|collection date:missing", "dataset3 BMPi LDN no RFP", "We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS", "dorsal fin", null, "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3\u2019 solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "tissue:dorsal fin|genotype:wild type|treatment:LDN", "GSM8635056", "GSM8635056: dataset3 BMPi LDN no RFP; Danio rerio; RNA Seq", "GSM8635056 r1", "GSM8635056", "1", "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP545529", null, "loader:fastq load.py", "LDN_noRFP_S3_L001_I1_001.fastq.gz LDN_noRFP_S3_L001_I2_001.fastq.gz LDN_noRFP_S3_L001_R1_001.fastq.gz LDN_noRFP_S3_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 5062759908.0, 36686666.0, "GSM8635056 r1", "0:10 1:10 2:28 3:90", "A:992393338;C:660757137;G:728422640;T:919955090;N:271735", 10, 10, 28, 90, 992393338, 660757137, 728422640, 919955090, 271735, "SRX26737887", "SRS23227908", "SRA2016042", "UVA", "UVA", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Unknown", "2024-11-15", "Undetermined", "Embryo", "Fin", "Surface Structure"], [34145, "SRR31364123", "SRX26737886", "SRS23227906", "SRP545529", "PRJNA1186739", "Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish", "GSE282061", "Transcriptome Analysis", "The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  \u201cmelanoleucophores.\u201d To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.", null, "pubmed:40305763", null, "dataset3 BMPi DMSO RFP", "GSM8635055", null, "source name:dorsal fin|tissue:dorsal fin|genotype:wild type|treatment:DMSO|geo loc name:missing|collection date:missing", "dataset3 BMPi DMSO RFP", "We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS", "dorsal fin", null, "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3\u2019 solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "tissue:dorsal fin|genotype:wild type|treatment:DMSO", "GSM8635055", "GSM8635055: dataset3 BMPi DMSO RFP; Danio rerio; RNA Seq", "GSM8635055 r1", "GSM8635055", "1", "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP545529", null, "loader:fastq load.py", "DMSO_RFP_S2_L001_I1_001.fastq.gz DMSO_RFP_S2_L001_I2_001.fastq.gz DMSO_RFP_S2_L001_R1_001.fastq.gz DMSO_RFP_S2_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 4298328228.0, 31147306.0, "GSM8635055 r1", "0:10 1:10 2:28 3:90", "A:816881516;C:611689038;G:673484940;T:700975488;N:226558", 10, 10, 28, 90, 816881516, 611689038, 673484940, 700975488, 226558, "SRX26737886", "SRS23227906", "SRA2016042", "UVA", "UVA", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Unknown", "2024-11-15", "Undetermined", "Embryo", "Fin", "Surface Structure"], [34146, "SRR31364124", "SRX26737885", "SRS23227907", "SRP545529", "PRJNA1186739", "Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish", "GSE282061", "Transcriptome Analysis", "The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  \u201cmelanoleucophores.\u201d To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.", null, "pubmed:40305763", null, "dataset3 BMPi DMSO no RFP", "GSM8635054", null, "source name:dorsal fin|tissue:dorsal fin|genotype:wild type|treatment:DMSO|geo loc name:missing|collection date:missing", "dataset3 BMPi DMSO no RFP", "We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS", "dorsal fin", null, "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3\u2019 solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "tissue:dorsal fin|genotype:wild type|treatment:DMSO", "GSM8635054", "GSM8635054: dataset3 BMPi DMSO no RFP; Danio rerio; RNA Seq", "GSM8635054 r1", "GSM8635054", "1", "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP545529", null, "loader:fastq load.py", "DMSO_noRFP_S1_L001_I1_001.fastq.gz DMSO_noRFP_S1_L001_I2_001.fastq.gz DMSO_noRFP_S1_L001_R1_001.fastq.gz DMSO_noRFP_S1_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 4086026820.0, 29608890.0, "GSM8635054 r1", "0:10 1:10 2:28 3:90", "A:794711851;C:543564325;G:594229898;T:732076441;N:217585", 10, 10, 28, 90, 794711851, 543564325, 594229898, 732076441, 217585, "SRX26737885", "SRS23227907", "SRA2016042", "UVA", "UVA", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Unknown", "2024-11-15", "Undetermined", "Embryo", "Fin", "Surface Structure"], [34147, "SRR31364125", "SRX26737884", "SRS23227904", "SRP545529", "PRJNA1186739", "Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish", "GSE282061", "Transcriptome Analysis", "The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  \u201cmelanoleucophores.\u201d To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.", null, "pubmed:40305763", null, "dataset2 positions base", "GSM8635053", null, "source name:dorsal fin|tissue:dorsal fin|genotype:wild type|geo loc name:missing|collection date:missing", "dataset2 positions base", "We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS", "dorsal fin", null, "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3\u2019 solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "tissue:dorsal fin|genotype:wild type", "GSM8635053", "GSM8635053: dataset2 positions base; Danio rerio; RNA Seq", "GSM8635053 r1", "GSM8635053", "1", "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP545529", null, "loader:fastq load.py", "tip_rest_S3_L001_I1_001.fastq.gz tip_rest_S3_L001_R1_001.fastq.gz tip_rest_S3_L001_R2_001.fastq.gz", "fastq fastq fastq", 2562938024.0, 27858022.0, "GSM8635053 r1", "0:8 1:28 2:56", "A:465025810;C:315982726;G:357090865;T:420656906;N:1292925", 8, 28, 56, null, 465025810, 315982726, 357090865, 420656906, 1292925, "SRX26737884", "SRS23227904", "SRA2016042", "UVA", "UVA", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Unknown", "2024-11-15", "Undetermined", "Embryo", "Fin", "Surface Structure"], [34148, "SRR31364126", "SRX26737883", "SRS23227905", "SRP545529", "PRJNA1186739", "Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish", "GSE282061", "Transcriptome Analysis", "The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  \u201cmelanoleucophores.\u201d To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.", null, "pubmed:40305763", null, "dataset2 positions edge", "GSM8635052", null, "source name:dorsal fin|tissue:dorsal fin|genotype:wild type|geo loc name:missing|collection date:missing", "dataset2 positions edge", "We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS", "dorsal fin", null, "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3\u2019 solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "tissue:dorsal fin|genotype:wild type", "GSM8635052", "GSM8635052: dataset2 positions edge; Danio rerio; RNA Seq", "GSM8635052 r1", "GSM8635052", "1", "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP545529", null, "loader:fastq load.py", "tip_white_S2_L001_I1_001.fastq.gz tip_white_S2_L001_R1_001.fastq.gz tip_white_S2_L001_R2_001.fastq.gz", "fastq fastq fastq", 3561960136.0, 38716958.0, "GSM8635052 r1", "0:8 1:28 2:56", "A:640222776;C:444619403;G:502208963;T:579280385;N:1818121", 8, 28, 56, null, 640222776, 444619403, 502208963, 579280385, 1818121, "SRX26737883", "SRS23227905", "SRA2016042", "UVA", "UVA", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Unknown", "2024-11-15", "Undetermined", "Embryo", "Fin", "Surface Structure"], [34149, "SRR31364127", "SRX26737882", "SRS23227903", "SRP545529", "PRJNA1186739", "Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish", "GSE282061", "Transcriptome Analysis", "The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  \u201cmelanoleucophores.\u201d To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.", null, "pubmed:40305763", null, "dataset1 stages rep4", "GSM8635051", null, "source name:dorsal fin|tissue:dorsal fin|genotype:wild type|geo loc name:missing|collection date:missing", "dataset1 stages rep4", "We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS", "dorsal fin", null, "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3\u2019 solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "tissue:dorsal fin|genotype:wild type", "GSM8635051", "GSM8635051: dataset1 stages rep4; Danio rerio; RNA Seq", "GSM8635051 r1", "GSM8635051", "1", "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP545529", null, "loader:fastq load.py", "dorsal_4_S4_L001_I1_001.fastq.gz dorsal_4_S4_L001_R1_001.fastq.gz dorsal_4_S4_L001_R2_001.fastq.gz", "fastq fastq fastq", 2719423400.0, 29558950.0, "GSM8635051 r1", "0:8 1:28 2:56", "A:491347530;C:348666057;G:386184840;T:428683151;N:419622", 8, 28, 56, null, 491347530, 348666057, 386184840, 428683151, 419622, "SRX26737882", "SRS23227903", "SRA2016042", "UVA", "UVA", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Unknown", "2024-11-15", "Undetermined", "Embryo", "Fin", "Surface Structure"], [34150, "SRR31364128", "SRX26737881", "SRS23227902", "SRP545529", "PRJNA1186739", "Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish", "GSE282061", "Transcriptome Analysis", "The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  \u201cmelanoleucophores.\u201d To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.", null, "pubmed:40305763", null, "dataset1 stages rep3", "GSM8635050", null, "source name:dorsal fin|tissue:dorsal fin|genotype:wild type|geo loc name:missing|collection date:missing", "dataset1 stages rep3", "We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS", "dorsal fin", null, "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3\u2019 solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "tissue:dorsal fin|genotype:wild type", "GSM8635050", "GSM8635050: dataset1 stages rep3; Danio rerio; RNA Seq", "GSM8635050 r1", "GSM8635050", "1", "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP545529", null, "loader:fastq load.py", "dorsal_3_S3_L001_I1_001.fastq.gz dorsal_3_S3_L001_R1_001.fastq.gz dorsal_3_S3_L001_R2_001.fastq.gz", "fastq fastq fastq", 2602160384.0, 28284352.0, "GSM8635050 r1", "0:8 1:28 2:56", "A:469841004;C:333542050;G:367823398;T:412316065;N:401195", 8, 28, 56, null, 469841004, 333542050, 367823398, 412316065, 401195, "SRX26737881", "SRS23227902", "SRA2016042", "UVA", "UVA", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Unknown", "2024-11-15", "Undetermined", "Embryo", "Fin", "Surface Structure"], [34151, "SRR31364129", "SRX26737880", "SRS23227901", "SRP545529", "PRJNA1186739", "Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish", "GSE282061", "Transcriptome Analysis", "The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  \u201cmelanoleucophores.\u201d To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.", null, "pubmed:40305763", null, "dataset1 stages rep2", "GSM8635049", null, "source name:dorsal fin|tissue:dorsal fin|genotype:wild type|geo loc name:missing|collection date:missing", "dataset1 stages rep2", "We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS", "dorsal fin", null, "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3\u2019 solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "tissue:dorsal fin|genotype:wild type", "GSM8635049", "GSM8635049: dataset1 stages rep2; Danio rerio; RNA Seq", "GSM8635049 r1", "GSM8635049", "1", "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP545529", null, "loader:fastq load.py", "dorsal_2_S2_L001_I1_001.fastq.gz dorsal_2_S2_L001_R1_001.fastq.gz dorsal_2_S2_L001_R2_001.fastq.gz", "fastq fastq fastq", 3187245056.0, 34643968.0, "GSM8635049 r1", "0:8 1:28 2:56", "A:584729856;C:395297406;G:447424733;T:512111292;N:498921", 8, 28, 56, null, 584729856, 395297406, 447424733, 512111292, 498921, "SRX26737880", "SRS23227901", "SRA2016042", "UVA", "UVA", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Unknown", "2024-11-15", "Undetermined", "Embryo", "Fin", "Surface Structure"], [34152, "SRR31364130", "SRX26737879", "SRS23227900", "SRP545529", "PRJNA1186739", "Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish", "GSE282061", "Transcriptome Analysis", "The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  \u201cmelanoleucophores.\u201d To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.", null, "pubmed:40305763", null, "dataset1 stages rep1", "GSM8635048", null, "source name:dorsal fin|tissue:dorsal fin|genotype:wild type|geo loc name:missing|collection date:missing", "dataset1 stages rep1", "We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS", "dorsal fin", null, "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3\u2019 solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "tissue:dorsal fin|genotype:wild type", "GSM8635048", "GSM8635048: dataset1 stages rep1; Danio rerio; RNA Seq", "GSM8635048 r1", "GSM8635048", "1", "Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP545529", null, "loader:fastq load.py", "dorsal_1_S1_L001_I1_001.fastq.gz dorsal_1_S1_L001_R1_001.fastq.gz dorsal_1_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 2963326992.0, 32210076.0, "GSM8635048 r1", "0:8 1:28 2:56", "A:550098255;C:357880179;G:398034107;T:497290530;N:461185", 8, 28, 56, null, 550098255, 357880179, 398034107, 497290530, 461185, "SRX26737879", "SRS23227900", "SRA2016042", "UVA", "UVA", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Unknown", "2024-11-15", "Undetermined", "Embryo", "Fin", "Surface Structure"], [52209, "SRR8992787", "SRX5771765", "SRS4705624", "SRP194294", "PRJNA540521", "Fate plasticity and reprogramming in genetically distinct populations of Danio leucophores", "GSE130526", "Other", "Understanding genetic and cellular bases of adult form remains a fundamental goal at the intersection of developmental and evolutionary biology. The skin pigment cells of vertebrates  derived from embryonic neural crest  are a useful system for elucidating mechanisms of fate specification  pattern formation  and how particular phenotypes impact organismal behavior and ecology. In a survey of Danio fishes  including zebrafish Danio rerio  we identified two populations of white pigment cells\u2014leucophores\u2014one of which arises by transdifferentiation of adult melanophores and another that develops from a yellow/orange xanthophore like progenitor. Single cell transcriptomic  mutational  chemical and ultrastructural analyses of zebrafish leucophores revealed cell type specific chemical compositions  organelle configurations and genetic requirements. At the organismal level  we identified distinct physiological responses of leucophores during environmental background matching and we show that leucophore complement influences behavior. Together  our studies revealed new  independently arisen pigment cell types and mechanisms of fate acquisition in zebrafish  and illustrate how concerted analyses across hierarchical levels can provide insights into phenotypes and their evolution. Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform using zebrafish fin pigment cells FACs sorted for mCherry. For additional details see associated publication", null, "pubmed:31138706", null, "Zebrafish fin pigment cells", "GSM3741778", null, "tissue:Dorsal and anal fins|cell type:pigment cells|treatment:Untreated", "Zebrafish fin pigment cells", "Expression matrix files were generated using cellranger 10X genomics version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Genome build: GRCz11/danRer11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.", "Dorsal and anal fins", "Fins were amputated from fish expressing both pnp4a:palmmCherry and tyrp1b:palmmCherry. To approximately normalize capture of relevant cell types by quantity and improve the likelihood of recovering cells at intermediate states of differentiation  we extracted distal dorsal fin regions 10 mm standard length  SL; n=20 and proximal interstripe anal fin regions 14 mm SL; n=10. Tissue was enzymatically dissociated with Liberase 0.25 mg/mL in dPBS at 25\u00b0C for 15 min followed by manual trituration with a flame polished glass pipette for 5 min. Cell suspensions were then filtered through a 70 \u03bcm Nylon cell strainer to obtain a single cell suspension. Liberated cells were re suspended in 1% BSA / 5% FBS in dPBS and DAPI 0.1 \u03bcg/mL  15 min before FACS purification. All plastic and glass surfaces of cell contact were coated with 1% BSA in dPBS before to use. Prior to sorting for fluorescence levels  single cells were isolated by sequentially gating cells according to their SSC A vs. FSC A  FSC H vs FSC W and SSC H vs SSC W profiles according to standard flow cytometry practices. Cells with high levels of DAPI staining were excluded as dead or damaged. Cells from wild type zebrafish were used as negative control to determine gates for detection of mCherry and GFP fluorescence  and then cells from transgenic fish were purified according to these gates. All samples were kept on ice  except during Liberase incubation  and then sorted chilled.", "10X genomics V1 protocol following manufacturer recommendations.", "Fish were maintained at 28.5C with 10 h : 14 h light:dark conditions. Larvae were reared with marine rotifers supplemented with Artemac Aquafauna followed by Artemia and flake food. Adults were maintained on Artemia and flake food. Fish stocks of Danio rerio: WTABb  a derivative of inbred ABwp  Tgtyrp1b:palm mCherrywp.rt11  Tgpnp4a:palmmCherrywp.rt10", "cell type:pigment cells|treatment:Untreated", "GSM3741778", "GSM3741778: Zebrafish fin pigment cells; Danio rerio; RNA Seq", "GSM3741778", null, "1", "10X genomics V1 protocol following manufacturer recommendations.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP194294", null, null, "leucophore_S9_L003_R2_001.fastq.gz leucophore_S9_L004_R1_001.fastq.gz", "fastq fastq", 424061944.0, 10241510.0, "GSM3741778 r1", "0:26 1:57", "A:119042142;C:89897538;G:98172861;T:116716009;N:233394", 26, 57, null, null, 119042142, 89897538, 98172861, 116716009, 233394, "SRX5771765", "SRS4705624", "SRA881136", "GEO", "Parichy Lab, Biology, University of Washington", 1, 0.33934, null, 0.07693, null, 0.8742, null, 0.51425, null, 57, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-04-30", "Multi-stage", "Multi-stage", "Fin", "Surface Structure"], [55221, "SRR10182211", "SRX6902836", "SRS5434733", "SRP223244", "PRJNA574059", "Cellular diversity of the regenerating caudal fin", "GSE137971", "Transcriptome Analysis", "single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies  filtered through 40 \u00b5m cell strainers  and washed with 1\u00d7 Dulbecco's phosphate buffered saline DPBS\u20130.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging  alignment to zebrafish reference genome GRCz10  and feature counting based on Ensembl release 91 cellranger count.", null, "pubmed:32851162", null, "1dpa fin1 scRNA", "GSM4095395", null, "source name:1dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:1 day post amputation", "1dpa fin1 scRNA", "All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly  sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.", "1dpa caudal fin", null, "We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax\u2122 ICT  filtered through 40\u00b5m cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics", "Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility  with system water temperature at 28.5\u02daC  and a day night cycle controlled as 14 hr light/10 hr dark.", "strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:1 day post amputation", "GSM4095395", "GSM4095395: 1dpa fin1 scRNA; Danio rerio; RNA Seq", "GSM4095395", null, "1", "We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax\u2122 ICT  filtered through 40\u00b5m cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics", "GEO Accession:GSM4095395", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP223244", null, null, "1dpa1_S1_L002_R1_001.fastq.gz 1dpa1_S1_L002_R2_001.fastq.gz", "fastq fastq", 3515690517.0, 34808817.0, "GSM4095395 r1", "0:26 1:75", "A:1021208515;C:750623954;G:773148636;T:968849435;N:1859977", 26, 75, null, null, 1021208515, 750623954, 773148636, 968849435, 1859977, "SRX6902836", "SRS5434733", "SRA968154", "GEO", "Ting Wang, Genetics, Washington University St Louis", 2, 0.00195, 0.91495, 0.00089, 0.10966, 0.99699, 0.84855, 0.35643, 0.59738, 26, 75, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-09-25", "Adult", "Adult", "Fin", "Surface Structure"], [55222, "SRR10182210", "SRX6902835", "SRS5434732", "SRP223244", "PRJNA574059", "Cellular diversity of the regenerating caudal fin", "GSE137971", "Transcriptome Analysis", "single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies  filtered through 40 \u00b5m cell strainers  and washed with 1\u00d7 Dulbecco's phosphate buffered saline DPBS\u20130.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging  alignment to zebrafish reference genome GRCz10  and feature counting based on Ensembl release 91 cellranger count.", null, "pubmed:32851162", null, "preinjury fin2 scRNA", "GSM4095394", null, "source name:Preinjury caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury", "preinjury fin2 scRNA", "All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly  sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.", "Preinjury caudal fin", null, "We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax\u2122 ICT  filtered through 40\u00b5m cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics", "Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility  with system water temperature at 28.5\u02daC  and a day night cycle controlled as 14 hr light/10 hr dark.", "strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury", "GSM4095394", "GSM4095394: preinjury fin2 scRNA; Danio rerio; RNA Seq", "GSM4095394", null, "1", "We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax\u2122 ICT  filtered through 40\u00b5m cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics", "GEO Accession:GSM4095394", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP223244", null, null, "samp2_S2_L002_R2_001.fastq.gz samp2_S2_L002_R1_001.fastq.gz", "fastq fastq", 14313306001.0, 141715901.0, "GSM4095394 r1", "0:26 1:75", "A:4080921082;C:3121900376;G:3341495424;T:3761528384;N:7460735", 26, 75, null, null, 4080921082, 3121900376, 3341495424, 3761528384, 7460735, "SRX6902835", "SRS5434732", "SRA968154", "GEO", "Ting Wang, Genetics, Washington University St Louis", 2, 0.0029, 0.89943, 0.00115, 0.07948, 0.99543, 0.8714, 0.29607, 0.47916, 26, 75, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-09-25", "Adult", "Adult", "Fin", "Surface Structure"], [55223, "SRR10182209", "SRX6902834", "SRS5434731", "SRP223244", "PRJNA574059", "Cellular diversity of the regenerating caudal fin", "GSE137971", "Transcriptome Analysis", "single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies  filtered through 40 \u00b5m cell strainers  and washed with 1\u00d7 Dulbecco's phosphate buffered saline DPBS\u20130.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging  alignment to zebrafish reference genome GRCz10  and feature counting based on Ensembl release 91 cellranger count.", null, "pubmed:32851162", null, "preinjury fin1 scRNA", "GSM4095393", null, "source name:Preinjury caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury", "preinjury fin1 scRNA", "All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly  sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.", "Preinjury caudal fin", null, "We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax\u2122 ICT  filtered through 40\u00b5m cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics", "Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility  with system water temperature at 28.5\u02daC  and a day night cycle controlled as 14 hr light/10 hr dark.", "strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury", "GSM4095393", "GSM4095393: preinjury fin1 scRNA; Danio rerio; RNA Seq", "GSM4095393", null, "1", "We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax\u2122 ICT  filtered through 40\u00b5m cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics", "GEO Accession:GSM4095393", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP223244", null, null, "samp1_S1_L001_R1_001.fastq.gz samp1_S1_L001_R2_001.fastq.gz", "fastq fastq", 14610147425.0, 144654925.0, "GSM4095393 r1", "0:26 1:75", "A:4066051353;C:3189039694;G:3388950081;T:3856651906;N:109454391", 26, 75, null, null, 4066051353, 3189039694, 3388950081, 3856651906, 109454391, "SRX6902834", "SRS5434731", "SRA968154", "GEO", "Ting Wang, Genetics, Washington University St Louis", 2, 0.0024, 0.87757, 0.00072, 0.08379, 0.99504, 0.85269, 0.34276, 0.52515, 26, 75, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-09-25", "Adult", "Adult", "Fin", "Surface Structure"], [55224, "SRR10182216", "SRX6902833", "SRS5434730", "SRP223244", "PRJNA574059", "Cellular diversity of the regenerating caudal fin", "GSE137971", "Transcriptome Analysis", "single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies  filtered through 40 \u00b5m cell strainers  and washed with 1\u00d7 Dulbecco's phosphate buffered saline DPBS\u20130.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging  alignment to zebrafish reference genome GRCz10  and feature counting based on Ensembl release 91 cellranger count.", null, "pubmed:32851162", null, "4dpa fin2 scRNA", "GSM4095400", null, "source name:4dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:4 day post amputation", "4dpa fin2 scRNA", "All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly  sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.", "4dpa caudal fin", null, "We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax\u2122 ICT  filtered through 40\u00b5m cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics", "Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility  with system water temperature at 28.5\u02daC  and a day night cycle controlled as 14 hr light/10 hr dark.", "strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:4 day post amputation", "GSM4095400", "GSM4095400: 4dpa fin2 scRNA; Danio rerio; RNA Seq", "GSM4095400", null, "1", "We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax\u2122 ICT  filtered through 40\u00b5m cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics", "GEO Accession:GSM4095400", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP223244", null, null, "4dpa2_S2_L002_R1_001.fastq.gz 4dpa2_S2_L002_R2_001.fastq.gz", "fastq fastq", 12205232082.0, 120843882.0, "GSM4095400 r1", "0:26 1:75", "A:3462691218;C:2662402586;G:2782962664;T:3293833482;N:3342132", 26, 75, null, null, 3462691218, 2662402586, 2782962664, 3293833482, 3342132, "SRX6902833", "SRS5434730", "SRA968154", "GEO", "Ting Wang, Genetics, Washington University St Louis", 2, 0.00216, 0.90418, 0.00058, 0.09381, 0.99488, 0.82666, 0.33993, 0.51619, 26, 75, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-09-25", "Adult", "Adult", "Fin", "Surface Structure"], [55225, "SRR10182215", "SRX6902832", "SRS5434729", "SRP223244", "PRJNA574059", "Cellular diversity of the regenerating caudal fin", "GSE137971", "Transcriptome Analysis", "single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies  filtered through 40 \u00b5m cell strainers  and washed with 1\u00d7 Dulbecco's phosphate buffered saline DPBS\u20130.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging  alignment to zebrafish reference genome GRCz10  and feature counting based on Ensembl release 91 cellranger count.", null, "pubmed:32851162", null, "4dpa fin1 scRNA", "GSM4095399", null, "source name:4dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:4 day post amputation", "4dpa fin1 scRNA", "All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly  sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.", "4dpa caudal fin", null, "We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax\u2122 ICT  filtered through 40\u00b5m cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics", "Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility  with system water temperature at 28.5\u02daC  and a day night cycle controlled as 14 hr light/10 hr dark.", "strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:4 day post amputation", "GSM4095399", "GSM4095399: 4dpa fin1 scRNA; Danio rerio; RNA Seq", "GSM4095399", null, "1", "We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax\u2122 ICT  filtered through 40\u00b5m cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics", "GEO Accession:GSM4095399", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP223244", null, null, "4dpa1_S1_L001_R1_001.fastq.gz 4dpa1_S1_L001_R2_001.fastq.gz", "fastq fastq", 14335848494.0, 141939094.0, "GSM4095399 r1", "0:26 1:75", "A:4028586492;C:3145713740;G:3334469278;T:3823390760;N:3688224", 26, 75, null, null, 4028586492, 3145713740, 3334469278, 3823390760, 3688224, "SRX6902832", "SRS5434729", "SRA968154", "GEO", "Ting Wang, Genetics, Washington University St Louis", 2, 0.00214, 0.90496, 0.00068, 0.10148, 0.99494, 0.82014, 0.36363, 0.54339, 26, 75, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-09-25", "Adult", "Adult", "Fin", "Surface Structure"], [55226, "SRR10182214", "SRX6902831", "SRS5434728", "SRP223244", "PRJNA574059", "Cellular diversity of the regenerating caudal fin", "GSE137971", "Transcriptome Analysis", "single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies  filtered through 40 \u00b5m cell strainers  and washed with 1\u00d7 Dulbecco's phosphate buffered saline DPBS\u20130.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging  alignment to zebrafish reference genome GRCz10  and feature counting based on Ensembl release 91 cellranger count.", null, "pubmed:32851162", null, "2dpa fin2 scRNA", "GSM4095398", null, "source name:2dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:2 day post amputation", "2dpa fin2 scRNA", "All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly  sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.", "2dpa caudal fin", null, "We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax\u2122 ICT  filtered through 40\u00b5m cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics", "Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility  with system water temperature at 28.5\u02daC  and a day night cycle controlled as 14 hr light/10 hr dark.", "strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:2 day post amputation", "GSM4095398", "GSM4095398: 2dpa fin2 scRNA; Danio rerio; RNA Seq", "GSM4095398", null, "1", "We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax\u2122 ICT  filtered through 40\u00b5m cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics", "GEO Accession:GSM4095398", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP223244", null, null, "2dpa2_S2_L002_R1_001.fastq.gz 2dpa2_S2_L002_R2_001.fastq.gz", "fastq fastq", 14592805725.0, 144483225.0, "GSM4095398 r1", "0:26 1:75", "A:4087287462;C:3228369053;G:3401290297;T:3861324848;N:14534065", 26, 75, null, null, 4087287462, 3228369053, 3401290297, 3861324848, 14534065, "SRX6902831", "SRS5434728", "SRA968154", "GEO", "Ting Wang, Genetics, Washington University St Louis", 2, 0.00231, 0.91223, 0.00055, 0.08705, 0.99452, 0.82627, 0.30769, 0.5211, 26, 75, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-09-25", "Adult", "Adult", "Fin", "Surface Structure"], [55227, "SRR10182213", "SRX6902830", "SRS5434727", "SRP223244", "PRJNA574059", "Cellular diversity of the regenerating caudal fin", "GSE137971", "Transcriptome Analysis", "single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies  filtered through 40 \u00b5m cell strainers  and washed with 1\u00d7 Dulbecco's phosphate buffered saline DPBS\u20130.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging  alignment to zebrafish reference genome GRCz10  and feature counting based on Ensembl release 91 cellranger count.", null, "pubmed:32851162", null, "2dpa fin1 scRNA", "GSM4095397", null, "source name:2dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:2 day post amputation", "2dpa fin1 scRNA", "All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly  sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.", "2dpa caudal fin", null, "We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax\u2122 ICT  filtered through 40\u00b5m cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics", "Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility  with system water temperature at 28.5\u02daC  and a day night cycle controlled as 14 hr light/10 hr dark.", "strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:2 day post amputation", "GSM4095397", "GSM4095397: 2dpa fin1 scRNA; Danio rerio; RNA Seq", "GSM4095397", null, "1", "We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax\u2122 ICT  filtered through 40\u00b5m cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics", "GEO Accession:GSM4095397", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP223244", null, null, "2dpa1_S1_L001_R1_001.fastq.gz 2dpa1_S1_L001_R2_001.fastq.gz", "fastq fastq", 15317979261.0, 151663161.0, "GSM4095397 r1", "0:26 1:75", "A:4303056842;C:3349998898;G:3533853775;T:4116083703;N:14986043", 26, 75, null, null, 4303056842, 3349998898, 3533853775, 4116083703, 14986043, "SRX6902830", "SRS5434727", "SRA968154", "GEO", "Ting Wang, Genetics, Washington University St Louis", 2, 0.0022, 0.9122, 0.0006, 0.09555, 0.99504, 0.82203, 0.33222, 0.52299, 26, 75, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-09-25", "Adult", "Adult", "Fin", "Surface Structure"], [55228, "SRR10182212", "SRX6902829", "SRS5434726", "SRP223244", "PRJNA574059", "Cellular diversity of the regenerating caudal fin", "GSE137971", "Transcriptome Analysis", "single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies  filtered through 40 \u00b5m cell strainers  and washed with 1\u00d7 Dulbecco's phosphate buffered saline DPBS\u20130.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging  alignment to zebrafish reference genome GRCz10  and feature counting based on Ensembl release 91 cellranger count.", null, "pubmed:32851162", null, "1dpa fin2 scRNA", "GSM4095396", null, "source name:1dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:1 day post amputation", "1dpa fin2 scRNA", "All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly  sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.", "1dpa caudal fin", null, "We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax\u2122 ICT  filtered through 40\u00b5m cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics", "Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility  with system water temperature at 28.5\u02daC  and a day night cycle controlled as 14 hr light/10 hr dark.", "strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:1 day post amputation", "GSM4095396", "GSM4095396: 1dpa fin2 scRNA; Danio rerio; RNA Seq", "GSM4095396", null, "1", "We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax\u2122 ICT  filtered through 40\u00b5m cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics", "GEO Accession:GSM4095396", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP223244", null, null, "1dpa2_S2_L002_R2_001.fastq.gz 1dpa2_S2_L002_R1_001.fastq.gz", "fastq fastq", 10934230609.0, 108259709.0, "GSM4095396 r1", "0:26 1:75", "A:3111673507;C:2358969825;G:2438293271;T:3019487882;N:5806124", 26, 75, null, null, 3111673507, 2358969825, 2438293271, 3019487882, 5806124, "SRX6902829", "SRS5434726", "SRA968154", "GEO", "Ting Wang, Genetics, Washington University St Louis", 2, 0.00198, 0.92416, 0.00054, 0.08626, 0.99596, 0.83808, 0.29818, 0.52586, 26, 75, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-09-25", "Adult", "Adult", "Fin", "Surface Structure"], [61429, "SRR12749699", "SRX9221655", "SRS7455356", "SRP285950", "PRJNA666695", "Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae", "GSE158851", "Transcriptome Analysis", "Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation.  Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform  and sequenced using Illumina NovaSeq 6000.  Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets  previously described by our group to govern zebrafish fin regeneration  and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform  and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.", null, "pubmed:34732706;pubmed:35664055", null, "Uncut caudal fin scRNA", "GSM4812244", null, "source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation", "Uncut caudal fin scRNA", "Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format\u00a0: the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination\u00a0; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv  barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'.", "caudal fin", null, "Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/\u03bcl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer\u2019s instructions using Chromium\u2122 Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.", null, "tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation", "GSM4812244", "GSM4812244: Uncut caudal fin scRNA; Danio rerio; RNA Seq", "GSM4812244", null, "1", "Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/\u03bcl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium\u2122 Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.", "GEO Accession:GSM4812244", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP285950", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=Uncut S8 L001 R1 001.fastq.gz   read2PairFiles=Uncut S8 L001 R2 001.fastq.gz   read3PairFiles=Uncut S8 L001 I1 001.fastq.gz", "Uncut_S8_L001_I1_001.fastq.gz Uncut_S8_L001_R1_001.fastq.gz Uncut_S8_L001_R2_001.fastq.gz", "fastq fastq fastq", 18909629967.0, 153736829.0, "GSM4812244 r1", "0:28 1:87 2:8", "A:5220924848;C:4279280050;G:4788532540;T:4619612909;N:1279620", 28, 87, 8, null, 5220924848, 4279280050, 4788532540, 4619612909, 1279620, "SRX9221655", "SRS7455356", "SRA1136463", "GEO", "Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm", 1, 0.63376, null, 0.11724, null, 0.8393, null, 0.55679, null, 87, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "France", "2020-09-30", "Larval", "Larval", "Fin", "Surface Structure"], [61430, "SRR12749700", "SRX9221655", "SRS7455356", "SRP285950", "PRJNA666695", "Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae", "GSE158851", "Transcriptome Analysis", "Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation.  Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform  and sequenced using Illumina NovaSeq 6000.  Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets  previously described by our group to govern zebrafish fin regeneration  and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform  and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.", null, "pubmed:34732706;pubmed:35664055", null, "Uncut caudal fin scRNA", "GSM4812244", null, "source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation", "Uncut caudal fin scRNA", "Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format\u00a0: the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination\u00a0; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv  barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'.", "caudal fin", null, "Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/\u03bcl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer\u2019s instructions using Chromium\u2122 Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.", null, "tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation", "GSM4812244", "GSM4812244: Uncut caudal fin scRNA; Danio rerio; RNA Seq", "GSM4812244", null, "1", "Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/\u03bcl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium\u2122 Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.", "GEO Accession:GSM4812244", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP285950", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=Uncut S8 L002 R1 001.fastq.gz   read2PairFiles=Uncut S8 L002 R2 001.fastq.gz   read3PairFiles=Uncut S8 L002 I1 001.fastq.gz", "Uncut_S8_L002_I1_001.fastq.gz Uncut_S8_L002_R1_001.fastq.gz Uncut_S8_L002_R2_001.fastq.gz", "fastq fastq fastq", 18967585107.0, 154208009.0, "GSM4812244 r2", "0:28 1:87 2:8", "A:5236542259;C:4292274179;G:4804216460;T:4633355352;N:1196857", 28, 87, 8, null, 5236542259, 4292274179, 4804216460, 4633355352, 1196857, "SRX9221655", "SRS7455356", "SRA1136463", "GEO", "Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm", 1, 0.63437, null, 0.11726, null, 0.83857, null, 0.5661, null, 87, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "France", "2020-09-30", "Larval", "Larval", "Fin", "Surface Structure"], [61431, "SRR12749697", "SRX9221654", "SRS7455355", "SRP285950", "PRJNA666695", "Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae", "GSE158851", "Transcriptome Analysis", "Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation.  Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform  and sequenced using Illumina NovaSeq 6000.  Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets  previously described by our group to govern zebrafish fin regeneration  and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform  and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.", null, "pubmed:34732706;pubmed:35664055", null, "Cut caudal fin scRNA", "GSM4812243", null, "source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours", "Cut caudal fin scRNA", "Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format\u00a0: the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination\u00a0; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv  barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'.", "caudal fin", null, "Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/\u03bcl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer\u2019s instructions using Chromium\u2122 Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.", null, "tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours", "GSM4812243", "GSM4812243: Cut caudal fin scRNA; Danio rerio; RNA Seq", "GSM4812243", null, "1", "Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/\u03bcl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium\u2122 Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.", "GEO Accession:GSM4812243", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP285950", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=Cut S7 L001 R1 001.fastq.gz   read2PairFiles=Cut S7 L001 R2 001.fastq.gz   read3PairFiles=Cut S7 L001 I1 001.fastq.gz", "Cut_S7_L001_I1_001.fastq.gz Cut_S7_L001_R1_001.fastq.gz Cut_S7_L001_R2_001.fastq.gz", "fastq fastq fastq", 17453571711.0, 141898957.0, "GSM4812243 r1", "0:28 1:87 2:8", "A:4820960991;C:3908308491;G:4347557585;T:4375565175;N:1179469", 28, 87, 8, null, 4820960991, 3908308491, 4347557585, 4375565175, 1179469, "SRX9221654", "SRS7455355", "SRA1136463", "GEO", "Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm", 1, 0.63902, null, 0.11232, null, 0.82235, null, 0.50797, null, 87, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "France", "2020-09-30", "Larval", "Larval", "Fin", "Surface Structure"], [61432, "SRR12749698", "SRX9221654", "SRS7455355", "SRP285950", "PRJNA666695", "Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae", "GSE158851", "Transcriptome Analysis", "Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation.  Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform  and sequenced using Illumina NovaSeq 6000.  Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets  previously described by our group to govern zebrafish fin regeneration  and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform  and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.", null, "pubmed:34732706;pubmed:35664055", null, "Cut caudal fin scRNA", "GSM4812243", null, "source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours", "Cut caudal fin scRNA", "Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format\u00a0: the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination\u00a0; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv  barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'.", "caudal fin", null, "Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/\u03bcl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer\u2019s instructions using Chromium\u2122 Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.", null, "tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours", "GSM4812243", "GSM4812243: Cut caudal fin scRNA; Danio rerio; RNA Seq", "GSM4812243", null, "1", "Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/\u03bcl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium\u2122 Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.", "GEO Accession:GSM4812243", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP285950", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=Cut S7 L002 R1 001.fastq.gz   read2PairFiles=Cut S7 L002 R2 001.fastq.gz   read3PairFiles=Cut S7 L002 I1 001.fastq.gz", "Cut_S7_L002_I1_001.fastq.gz Cut_S7_L002_R1_001.fastq.gz Cut_S7_L002_R2_001.fastq.gz", "fastq fastq fastq", 17511283926.0, 142368162.0, "GSM4812243 r2", "0:28 1:87 2:8", "A:4836849959;C:3920920286;G:4362769830;T:4389644044;N:1099807", 28, 87, 8, null, 4836849959, 3920920286, 4362769830, 4389644044, 1099807, "SRX9221654", "SRS7455355", "SRA1136463", "GEO", "Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm", 1, 0.63847, null, 0.11249, null, 0.82231, null, 0.51524, null, 87, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "France", "2020-09-30", "Larval", "Larval", "Fin", "Surface Structure"], [65589, "SRR15390211", "SRX11692441", "SRS9724035", "SRP331755", "PRJNA753151", "scRNA seq of fin and body zebrafish melanocytes", "GSE181748", "Transcriptome Analysis", "Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here  we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body  whereas the acral subtype arises on the palms of the hands  soles of the feet  or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs  indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes  compared to body melanocytes  revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma  which was generated by injecting Casper fish with MniCoopR GFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins  digested using liberase  and then FACS sorted for GFP+ melanocytes and GFP  microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total  GFP+ body cells  GFP  body cells  GFP+ fin cells  GFP  fin cells. Data was then analyzed and pooled together  taking note of their sample origin.", null, "pubmed:35355015", null, "XFN", "GSM5510267", null, "source name:Zebrafish fins|model:Acral melanoma model Caspers with MiniCoopR eGFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6 nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP ", "XFN", "Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao  Hao et al.  2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija  2019. Principal component analysis Joliffe  1986 and UMAP dimensionality reduction McInnes  2018 were performed using default parameters  with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al.  2020; Hunter  Moncada et al.  2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output", "Zebrafish fins", 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:Fin|cell type:GFP ", "GSM5510267", "GSM5510267: XFN; Danio rerio; RNA Seq", "GSM5510267", 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:GSM5510267", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP331755", null, null, "2385_XFN_IGO_11718_4_S4_L001_R1_001.fastq.gz 2385_XFN_IGO_11718_4_S4_L001_R2_001.fastq.gz", "fastq fastq", 20452607604.0, 174808612.0, "GSM5510267 r1", "0:29 1:88", "A:5729911089;C:4526353776;G:4631244451;T:5564405432;N:692856", 29, 88, null, null, 5729911089, 4526353776, 4631244451, 5564405432, 692856, "SRX11692441", "SRS9724035", "SRA1274997", "GEO", "White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.00608, 0.85139, 0.00196, 0.14282, 0.99093, 0.78543, 0.42676, 0.53168, 29, 88, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-09", "Undetermined", "Adult", "Fin", "Surface Structure"], [65590, "SRR15390212", "SRX11692441", "SRS9724035", "SRP331755", "PRJNA753151", "scRNA seq of fin and body zebrafish melanocytes", "GSE181748", "Transcriptome Analysis", "Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here  we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body  whereas the acral subtype arises on the palms of the hands  soles of the feet  or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs  indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes  compared to body melanocytes  revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma  which was generated by injecting Casper fish with MniCoopR GFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins  digested using liberase  and then FACS sorted for GFP+ melanocytes and GFP  microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total  GFP+ body cells  GFP  body cells  GFP+ fin cells  GFP  fin cells. Data was then analyzed and pooled together  taking note of their sample origin.", null, "pubmed:35355015", null, "XFN", "GSM5510267", null, "source name:Zebrafish fins|model:Acral melanoma model Caspers with MiniCoopR eGFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6 nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP ", "XFN", "Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao  Hao et al.  2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija  2019. Principal component analysis Joliffe  1986 and UMAP dimensionality reduction McInnes  2018 were performed using default parameters  with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al.  2020; Hunter  Moncada et al.  2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output", "Zebrafish fins", 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:Fin|cell type:GFP ", "GSM5510267", "GSM5510267: XFN; Danio rerio; RNA Seq", "GSM5510267", 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:GSM5510267", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP331755", null, null, "2385_XFN_IGO_11718_4_S4_L002_R1_001.fastq.gz 2385_XFN_IGO_11718_4_S4_L002_R2_001.fastq.gz", "fastq fastq", 20056571028.0, 171423684.0, "GSM5510267 r2", "0:29 1:88", "A:5624358913;C:4435209829;G:4536840173;T:5459497012;N:665101", 29, 88, null, null, 5624358913, 4435209829, 4536840173, 5459497012, 665101, "SRX11692441", "SRS9724035", "SRA1274997", "GEO", "White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.00636, 0.85263, 0.00229, 0.14314, 0.99113, 0.78206, 0.42564, 0.53095, 29, 88, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-09", "Undetermined", "Adult", "Fin", "Surface Structure"], [65591, "SRR15390209", "SRX11692439", "SRS9724039", "SRP331755", "PRJNA753151", "scRNA seq of fin and body zebrafish melanocytes", "GSE181748", "Transcriptome Analysis", "Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here  we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body  whereas the acral subtype arises on the palms of the hands  soles of the feet  or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs  indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes  compared to body melanocytes  revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma  which was generated by injecting Casper fish with MniCoopR GFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins  digested using liberase  and then FACS sorted for GFP+ melanocytes and GFP  microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total  GFP+ body cells  GFP  body cells  GFP+ fin cells  GFP  fin cells. Data was then analyzed and pooled together  taking note of their sample origin.", null, "pubmed:35355015", null, "XFG", "GSM5510266", null, "source name:Zebrafish fins|model:Acral melanoma model Caspers with MiniCoopR eGFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6 nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP+", "XFG", "Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao  Hao et al.  2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija  2019. Principal component analysis Joliffe  1986 and UMAP dimensionality reduction McInnes  2018 were performed using default parameters  with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al.  2020; Hunter  Moncada et al.  2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output", "Zebrafish fins", 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:Fin|cell type:GFP+", "GSM5510266", "GSM5510266: XFG; Danio rerio; RNA Seq", "GSM5510266", 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:GSM5510266", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP331755", null, null, "2384_XFG_IGO_11718_3_S3_L001_R1_001.fastq.gz 2384_XFG_IGO_11718_3_S3_L001_R2_001.fastq.gz", "fastq fastq", 21239736102.0, 181536206.0, "GSM5510266 r1", "0:29 1:88", "A:6013451435;C:4631285818;G:4786546365;T:5807740759;N:711725", 29, 88, null, null, 6013451435, 4631285818, 4786546365, 5807740759, 711725, "SRX11692439", "SRS9724039", "SRA1274997", "GEO", "White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.00797, 0.89811, 0.00258, 0.14942, 0.9889, 0.79259, 0.38209, 0.54357, 29, 88, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-09", "Undetermined", "Adult", "Fin", "Surface Structure"], [65592, "SRR15390210", "SRX11692439", "SRS9724039", "SRP331755", "PRJNA753151", "scRNA seq of fin and body zebrafish melanocytes", "GSE181748", "Transcriptome Analysis", "Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here  we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body  whereas the acral subtype arises on the palms of the hands  soles of the feet  or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs  indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes  compared to body melanocytes  revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma  which was generated by injecting Casper fish with MniCoopR GFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins  digested using liberase  and then FACS sorted for GFP+ melanocytes and GFP  microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total  GFP+ body cells  GFP  body cells  GFP+ fin cells  GFP  fin cells. Data was then analyzed and pooled together  taking note of their sample origin.", null, "pubmed:35355015", null, "XFG", "GSM5510266", null, "source name:Zebrafish fins|model:Acral melanoma model Caspers with MiniCoopR eGFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6 nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP+", "XFG", "Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao  Hao et al.  2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija  2019. Principal component analysis Joliffe  1986 and UMAP dimensionality reduction McInnes  2018 were performed using default parameters  with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al.  2020; Hunter  Moncada et al.  2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output", "Zebrafish fins", 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:Fin|cell type:GFP+", "GSM5510266", "GSM5510266: XFG; Danio rerio; RNA Seq", "GSM5510266", 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:GSM5510266", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP331755", null, null, "2384_XFG_IGO_11718_3_S3_L002_R1_001.fastq.gz 2384_XFG_IGO_11718_3_S3_L002_R2_001.fastq.gz", "fastq fastq", 20799675234.0, 177775002.0, "GSM5510266 r2", "0:29 1:88", "A:5894902894;C:4531100030;G:4681582244;T:5691398362;N:691704", 29, 88, null, null, 5894902894, 4531100030, 4681582244, 5691398362, 691704, "SRX11692439", "SRS9724039", "SRA1274997", "GEO", "White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.00787, 0.89764, 0.00227, 0.14926, 0.98821, 0.78928, 0.40092, 0.53114, 29, 88, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-09", "Undetermined", "Adult", "Fin", "Surface Structure"], [71755, "SRR22013536", "SRX17995702", "SRS15506856", "SRP404046", "PRJNA893216", "Insulin like growth factor receptor / mTOR signaling elevates global translation to accelerate zebrafish fin regenerative outgrowth", "GSE216359", "Transcriptome Analysis", "We generate a single cell transcriptome dataset to characterize zebrafish fin regenerative outgrowth and explore coordinated cell behaviors. Overall design: Regenerated fin tissue was collected from 3 and 7 dy post amputation zebrafish caudal fins and analyzed using scRNA seq", null, "pubmed:37290497", null, "7 dpa  scRNA seq", "GSM6670935", null, "source name:Caudal fin|tissue:Caudal fin|time:7 dpa|genotype:Tgsp7:EGFP;Tgtph1b:mCherry|Stage:Adult|geo loc name:missing|collection date:missing", "7 dpa  scRNA seq", "Pseudoalignment and processing of raw reads was done in Kallisto/Bustools https://github.com/pachterlab/kb python to generate a cell data set for Monocle3 https://cole trapnell lab.github.io/monocle3/ Assembly: GRCz11.99 Supplementary files format and content: rds file of cell data set", "Caudal fin", null, "Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice  diced  then washed with L 15 media supplemented with 1X GlutaMax  1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml  Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 \u03bcm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. Library was performed according to the manufacturer\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics. Briefly  cells from fin tissue were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up  amplified by PCR  and the appropiate sized fragments were selected for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "tissue:Caudal fin|time:7 dpa|genotype:Tgsp7:EGFP;Tgtph1b:mCherry|Stage:Adult", "GSM6670935", "GSM6670935: 7 dpa  scRNA seq; Danio rerio; RNA Seq", "GSM6670935 r1", "GSM6670935", "1", "Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice  diced  then washed with L 15 media supplemented with 1X GlutaMax  1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml  Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 \u03bcm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. Library was performed according to the manufacturer's instructions single cell three prime v3 protocol  10x Genomics. Briefly  cells from fin tissue were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up  amplified by PCR  and the appropiate sized fragments were selected for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP404046", null, "loader:fastq load.py", "3668_7dpa_S2_L001_I1_001.fastq.gz 3668_7dpa_S2_L001_R1_001.fastq.gz 3668_7dpa_S2_L001_R2_001.fastq.gz", "fastq fastq fastq", 14309041035.0, 104445555.0, "GSM6670935 r1", "0:8 1:28 2:101", "A:3095734143;C:2218234178;G:2235474863;T:2997266454;N:2291417", 8, 28, 101, null, 3095734143, 2218234178, 2235474863, 2997266454, 2291417, "SRX17995702", "SRS15506856", "SRA1525679", "Stankunas, Institute of Molecular Biology, University of Oregon", "Stankunas, Institute of Molecular Biology, University of Oregon", 1, 0.89077, null, 0.20943, null, 0.79935, null, 0.6085, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-10-22", "Adult", "Adult", "Fin", "Surface Structure"], [71756, "SRR22013537", "SRX17995702", "SRS15506856", "SRP404046", "PRJNA893216", "Insulin like growth factor receptor / mTOR signaling elevates global translation to accelerate zebrafish fin regenerative outgrowth", "GSE216359", "Transcriptome Analysis", "We generate a single cell transcriptome dataset to characterize zebrafish fin regenerative outgrowth and explore coordinated cell behaviors. Overall design: Regenerated fin tissue was collected from 3 and 7 dy post amputation zebrafish caudal fins and analyzed using scRNA seq", null, "pubmed:37290497", null, "7 dpa  scRNA seq", "GSM6670935", null, "source name:Caudal fin|tissue:Caudal fin|time:7 dpa|genotype:Tgsp7:EGFP;Tgtph1b:mCherry|Stage:Adult|geo loc name:missing|collection date:missing", "7 dpa  scRNA seq", "Pseudoalignment and processing of raw reads was done in Kallisto/Bustools https://github.com/pachterlab/kb python to generate a cell data set for Monocle3 https://cole trapnell lab.github.io/monocle3/ Assembly: GRCz11.99 Supplementary files format and content: rds file of cell data set", "Caudal fin", null, "Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice  diced  then washed with L 15 media supplemented with 1X GlutaMax  1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml  Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 \u03bcm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. Library was performed according to the manufacturer\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics. Briefly  cells from fin tissue were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up  amplified by PCR  and the appropiate sized fragments were selected for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "tissue:Caudal fin|time:7 dpa|genotype:Tgsp7:EGFP;Tgtph1b:mCherry|Stage:Adult", "GSM6670935", "GSM6670935: 7 dpa  scRNA seq; Danio rerio; RNA Seq", "GSM6670935 r1", "GSM6670935", "1", "Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice  diced  then washed with L 15 media supplemented with 1X GlutaMax  1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml  Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 \u03bcm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. Library was performed according to the manufacturer's instructions single cell three prime v3 protocol  10x Genomics. Briefly  cells from fin tissue were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up  amplified by PCR  and the appropiate sized fragments were selected for subsequent library construction. 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Overall design: Regenerated fin tissue was collected from 3 and 7 dy post amputation zebrafish caudal fins and analyzed using scRNA seq", null, "pubmed:37290497", null, "3 dpa  scRNA seq", "GSM6670934", null, "source name:Caudal fin|tissue:Caudal fin|time:3 dpa|genotype:Tgsp7:EGFP;Tgtph1b:mCherry|Stage:Adult|geo loc name:missing|collection date:missing", "3 dpa  scRNA seq", "Pseudoalignment and processing of raw reads was done in Kallisto/Bustools https://github.com/pachterlab/kb python to generate a cell data set for Monocle3 https://cole trapnell lab.github.io/monocle3/ Assembly: GRCz11.99 Supplementary files format and content: rds file of cell data set", "Caudal fin", null, "Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice  diced  then washed with L 15 media supplemented with 1X GlutaMax  1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml  Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 \u03bcm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. Library was performed according to the manufacturer\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics. Briefly  cells from fin tissue were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up  amplified by PCR  and the appropiate sized fragments were selected for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "tissue:Caudal fin|time:3 dpa|genotype:Tgsp7:EGFP;Tgtph1b:mCherry|Stage:Adult", "GSM6670934", "GSM6670934: 3 dpa  scRNA seq; Danio rerio; RNA Seq", "GSM6670934 r1", "GSM6670934", "1", "Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice  diced  then washed with L 15 media supplemented with 1X GlutaMax  1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml  Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 \u03bcm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. 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Overall design: Regenerated fin tissue was collected from 3 and 7 dy post amputation zebrafish caudal fins and analyzed using scRNA seq", null, "pubmed:37290497", null, "3 dpa  scRNA seq", "GSM6670934", null, "source name:Caudal fin|tissue:Caudal fin|time:3 dpa|genotype:Tgsp7:EGFP;Tgtph1b:mCherry|Stage:Adult|geo loc name:missing|collection date:missing", "3 dpa  scRNA seq", "Pseudoalignment and processing of raw reads was done in Kallisto/Bustools https://github.com/pachterlab/kb python to generate a cell data set for Monocle3 https://cole trapnell lab.github.io/monocle3/ Assembly: GRCz11.99 Supplementary files format and content: rds file of cell data set", "Caudal fin", null, "Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice  diced  then washed with L 15 media supplemented with 1X GlutaMax  1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml  Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 \u03bcm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. Library was performed according to the manufacturer\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics. Briefly  cells from fin tissue were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up  amplified by PCR  and the appropiate sized fragments were selected for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "tissue:Caudal fin|time:3 dpa|genotype:Tgsp7:EGFP;Tgtph1b:mCherry|Stage:Adult", "GSM6670934", "GSM6670934: 3 dpa  scRNA seq; Danio rerio; RNA Seq", "GSM6670934 r1", "GSM6670934", "1", "Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice  diced  then washed with L 15 media supplemented with 1X GlutaMax  1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml  Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 \u03bcm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. Library was performed according to the manufacturer'", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP404046", null, "loader:fastq load.py", "3669_3dpa_S4_L002_I1_001.fastq.gz 3669_3dpa_S4_L002_R1_001.fastq.gz 3669_3dpa_S4_L002_R2_001.fastq.gz", "fastq fastq fastq", 18947450035.0, 138302555.0, "GSM6670934 r2", "0:8 1:28 2:101", "A:4126083375;C:2867407006;G:2991995583;T:3979778947;N:3293144", 8, 28, 101, null, 4126083375, 2867407006, 2991995583, 3979778947, 3293144, "SRX17995701", "SRS15506855", "SRA1525679", "Stankunas, Institute of Molecular Biology, University of Oregon", "Stankunas, Institute of Molecular Biology, University of Oregon", 1, 0.91921, null, 0.19517, null, 0.78524, null, 0.57129, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-10-22", "Adult", "Adult", "Fin", "Surface Structure"]], "truncated": 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