{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC SINGLE CELL\" 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"], [53593, "SRR11886700", "SRX8434172", "SRS6745285", "SRP265421", "PRJNA559885", "A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration", "PRJNA559885", "Other", "The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities  while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic  developmental  cellular and molecular studies  the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio  we uncovered species specific and evolutionarily conserved genomic responses to amputation.", null, null, null, "zebrafish fin regeneration", "zebrafish fin 1dpa", null, "strain:AB|isolate:12|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish blastema single cell", "L41598", "L41598", "The African killifish and zebrafish single cell RNA seq were done with the 10x Chromium platform. About 20 fish were used for cell dissociation in each experiment. Hoechst stained cells 100 000 cells from the dissected blastema tissues at 1dpa were collected on ice using a BD Influx sorter. The viability of cells 94.5% was determined before loading cells into 10x Chromium platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP265421", null, "loader:fastq load.py", "L41598_S1_L001_I1_001.fastq.gz L41598_S1_L001_R1_001.fastq.gz L41598_S1_L001_R2_001.fastq.gz L41598_S1_L002_I1_001.fastq.gz L41598_S1_L002_R1_001.fastq.gz L41598_S1_L002_R2_001.fastq.gz L41598_S1_L003_I1_001.fastq.gz L41598_S1_L003_R1_001.fastq.gz L41598_S1_L003_R2_001.fastq.gz L41598_S1_L004_I1_001.fastq.gz L41598_S1_L004_R1_001.fastq.gz L41598_S1_L004_R2_001.fastq.gz", "fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq", 52222012142.0, 411196946.0, "L41598 S1 L001 I1 001.fastq.gz", "0:8 1:28 2:91", "A:10978857897;C:7760934381;G:8557391299;T:10029401940;N:92336569", 8, 28, 91, null, 10978857897, 7760934381, 8557391299, 10029401940, 92336569, "SRX8434172", "SRS6745285", "SRA1081627", "Stowers Institute for Medical Research|Sanchez lab", "Stowers Institute for Medical Research", 1, 0.92629, null, 0.12539, null, 0.78589, null, 0.5225, null, 91, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-08-11", "Adult", "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. 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", "3668_3dpa_S1_L001_I1_001.fastq.gz 3668_3dpa_S1_L001_R1_001.fastq.gz 3668_3dpa_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 18445973865.0, 134642145.0, "GSM6670934 r1", "0:8 1:28 2:101", "A:4016744063;C:2790570873;G:2912735479;T:3875859487;N:2946743", 8, 28, 101, null, 4016744063, 2790570873, 2912735479, 3875859487, 2946743, "SRX17995701", "SRS15506855", "SRA1525679", "Stankunas, Institute of Molecular Biology, University of Oregon", "Stankunas, Institute of Molecular Biology, University of Oregon", 1, 0.92077, null, 0.19536, null, 0.78597, null, 0.5661, 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"], [71758, "SRR22013539", "SRX17995701", "SRS15506855", "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, "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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