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46 rows where experiment.platform = "ILLUMINA", technology = "10x" and tissue_curation = "Fin"

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devstage_curation_coarse 5

devstage_curation 4

experiment.library_source 2

experiment.library_selection 2

tissue_curation_coarse 1

tissue_curation 1

  • Fin · 46 ✖

technology 1

  • 10x · 46 ✖

experiment.platform 1

  • ILLUMINA · 46 ✖

experiment.library_strategy 1

experiment.library_layout 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
29197 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.   pubmed:38318374   4th round of regeneration GSM7988809   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°C. 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 µm cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2 Gibco #12082739. post centrifugation 15 minutes 1800 rpm 4°C the supernatant was discarded and the remaining cell pellet resuspended in 500 µl 2% BSA in PBS. Calcein violet 1µl 10mM Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet GFP and mCherry+ cells were collected in 50 µl 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 µl 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’ 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.   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 µl 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP479569     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     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   Germany 2023-12-21 Undetermined Undetermined Fin Surface Structure
29198 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.   pubmed:38318374   3rd round of regeneration GSM7988808   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°C. 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 µm cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2 Gibco #12082739. post centrifugation 15 minutes 1800 rpm 4°C the supernatant was discarded and the remaining cell pellet resuspended in 500 µl 2% BSA in PBS. Calcein violet 1µl 10mM Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet GFP and mCherry+ cells were collected in 50 µl 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 µl 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’ 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.   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 µl 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP479569     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     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   Germany 2023-12-21 Undetermined Undetermined Fin Surface Structure
29199 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.   pubmed:38318374   2nd round of regeneration GSM7988807   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°C. 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 µm cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2 Gibco #12082739. post centrifugation 15 minutes 1800 rpm 4°C the supernatant was discarded and the remaining cell pellet resuspended in 500 µl 2% BSA in PBS. Calcein violet 1µl 10mM Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet GFP and mCherry+ cells were collected in 50 µl 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 µl 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’ 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.   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 µl 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP479569     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     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   Germany 2023-12-21 Undetermined Undetermined Fin Surface Structure
29200 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.   pubmed:38318374   1st round of regeneration GSM7988806   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°C. 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 µm cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2 Gibco #12082739. post centrifugation 15 minutes 1800 rpm 4°C the supernatant was discarded and the remaining cell pellet resuspended in 500 µl 2% BSA in PBS. Calcein violet 1µl 10mM Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet GFP and mCherry+ cells were collected in 50 µl 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 µl 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’ 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.   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 µl 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP479569     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     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   Germany 2023-12-21 Undetermined Undetermined Fin Surface Structure
30628 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.   pubmed:39809530   6 day post amputation replicate 2 6dpa fin2   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                 6dpa fin2 snRNA 6dpa2 RNA 6dpa2 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     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     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   United States 2024-02-12 Adult Adult Fin Surface Structure
30629 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.   pubmed:39809530   6 day post amputation replicate 1 6dpa fin1   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                 6dpa fin1 snRNA 6dpa1 RNA 6dpa1 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     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     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   United States 2024-02-12 Adult Adult Fin Surface Structure
30630 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.   pubmed:39809530   4 day post amputation replicate 2 4dpa fin2   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                 4dpa fin2 snRNA 4dpa2 RNA 4dpa2 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     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     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   United States 2024-02-12 Adult Adult Fin Surface Structure
30631 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.   pubmed:39809530   4 day post amputation replicate 1 4dpa fin1   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                 4dpa fin1 snRNA 4dpa1 RNA 4dpa1 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     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     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   United States 2024-02-12 Adult Adult Fin Surface Structure
30632 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.   pubmed:39809530   2 day post amputation replicate 2 2dpa fin2   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                 2dpa fin2 snRNA 2dpa2 RNA 2dpa2 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     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     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   United States 2024-02-12 Adult Adult Fin Surface Structure
30633 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.   pubmed:39809530   2 day post amputation replicate 1 2dpa fin1   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                 2dpa fin1 snRNA 2dpa1 RNA 2dpa1 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     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     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   United States 2024-02-12 Adult Adult Fin Surface Structure
30634 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.   pubmed:39809530   1 day post amputation replicate 2 1dpa fin2   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                 1dpa fin2 snRNA 1dpa2 RNA 1dpa2 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     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     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   United States 2024-02-12 Adult Adult Fin Surface Structure
30635 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.   pubmed:39809530   1 day post amputation replicate 1 1dpa fin1   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                 1dpa fin1 snRNA 1dpa1 RNA 1dpa1 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     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     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   United States 2024-02-12 Adult Adult Fin Surface Structure
30636 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.   pubmed:39809530   0 day post amputation replicate 2 0dpa fin2   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                 0dpa fin2 snRNA 0dpa2 RNA 0dpa2 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     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     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   United States 2024-02-12 Adult Adult Fin Surface Structure
30637 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.   pubmed:39809530   0 day post amputation replicate 1 0dpa fin1   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                 0dpa fin1 snRNA 0dpa1 RNA 0dpa1 RNA Cadual fin tissue nuclei extraction 10x Genomics Chromium Single Cell Multiome     RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP489317     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     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   United States 2024-02-12 Adult Adult Fin Surface Structure
34143 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 “melanoleucophores.” 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.   pubmed:40305763   dataset3 BMPi LDN RFP GSM8635057   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   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’ 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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP545529   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                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Unknown 2024-11-15 Undetermined Embryo Fin Surface Structure
34144 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 “melanoleucophores.” 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.   pubmed:40305763   dataset3 BMPi LDN no RFP GSM8635056   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   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’ 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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP545529   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                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Unknown 2024-11-15 Undetermined Embryo Fin Surface Structure
34145 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 “melanoleucophores.” 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.   pubmed:40305763   dataset3 BMPi DMSO RFP GSM8635055   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   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’ 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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP545529   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                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Unknown 2024-11-15 Undetermined Embryo Fin Surface Structure
34146 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 “melanoleucophores.” 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.   pubmed:40305763   dataset3 BMPi DMSO no RFP GSM8635054   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   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’ 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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP545529   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                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Unknown 2024-11-15 Undetermined Embryo Fin Surface Structure
34147 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 “melanoleucophores.” 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.   pubmed:40305763   dataset2 positions base GSM8635053   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   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’ 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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP545529   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   465025810 315982726 357090865 420656906 1292925 SRX26737884 SRS23227904 SRA2016042 UVA UVA                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Unknown 2024-11-15 Undetermined Embryo Fin Surface Structure
34148 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 “melanoleucophores.” 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.   pubmed:40305763   dataset2 positions edge GSM8635052   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   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’ 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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP545529   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   640222776 444619403 502208963 579280385 1818121 SRX26737883 SRS23227905 SRA2016042 UVA UVA                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Unknown 2024-11-15 Undetermined Embryo Fin Surface Structure
34149 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 “melanoleucophores.” 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.   pubmed:40305763   dataset1 stages rep4 GSM8635051   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   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’ 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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP545529   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   491347530 348666057 386184840 428683151 419622 SRX26737882 SRS23227903 SRA2016042 UVA UVA                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Unknown 2024-11-15 Undetermined Embryo Fin Surface Structure
34150 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 “melanoleucophores.” 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.   pubmed:40305763   dataset1 stages rep3 GSM8635050   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   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’ 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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP545529   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   469841004 333542050 367823398 412316065 401195 SRX26737881 SRS23227902 SRA2016042 UVA UVA                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Unknown 2024-11-15 Undetermined Embryo Fin Surface Structure
34151 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 “melanoleucophores.” 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.   pubmed:40305763   dataset1 stages rep2 GSM8635049   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   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’ 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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP545529   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   584729856 395297406 447424733 512111292 498921 SRX26737880 SRS23227901 SRA2016042 UVA UVA                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Unknown 2024-11-15 Undetermined Embryo Fin Surface Structure
34152 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 “melanoleucophores.” 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.   pubmed:40305763   dataset1 stages rep1 GSM8635048   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   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’ 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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP545529   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   550098255 357880179 398034107 497290530 461185 SRX26737879 SRS23227900 SRA2016042 UVA UVA                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Unknown 2024-11-15 Undetermined Embryo Fin Surface Structure
52209 52209 SRR8992787 SRX5771765 SRS4705624 SRP194294 PRJNA540521 Fate plasticity and reprogramming in genetically distinct populations of Danio leucophores GSE130526 Other Understanding genetic and cellular bases of adult form remains a fundamental goal at the intersection of developmental and evolutionary biology. The skin pigment cells of vertebrates derived from embryonic neural crest are a useful system for elucidating mechanisms of fate specification pattern formation and how particular phenotypes impact organismal behavior and ecology. In a survey of Danio fishes including zebrafish Danio rerio we identified two populations of white pigment cells—leucophores—one of which arises by transdifferentiation of adult melanophores and another that develops from a yellow/orange xanthophore like progenitor. Single cell transcriptomic mutational chemical and ultrastructural analyses of zebrafish leucophores revealed cell type specific chemical compositions organelle configurations and genetic requirements. At the organismal level we identified distinct physiological responses of leucophores during environmental background matching and we show that leucophore complement influences behavior. Together our studies revealed new independently arisen pigment cell types and mechanisms of fate acquisition in zebrafish and illustrate how concerted analyses across hierarchical levels can provide insights into phenotypes and their evolution. Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform using zebrafish fin pigment cells FACs sorted for mCherry. For additional details see associated publication   pubmed:31138706   Zebrafish fin pigment cells GSM3741778   tissue:Dorsal and anal fins|cell type:pigment cells|treatment:Untreated Zebrafish fin pigment cells Expression matrix files were generated using cellranger 10X genomics version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Genome build: GRCz11/danRer11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. Dorsal and anal fins Fins were amputated from fish expressing both pnp4a:palmmCherry and tyrp1b:palmmCherry. To approximately normalize capture of relevant cell types by quantity and improve the likelihood of recovering cells at intermediate states of differentiation we extracted distal dorsal fin regions 10 mm standard length SL; n=20 and proximal interstripe anal fin regions 14 mm SL; n=10. Tissue was enzymatically dissociated with Liberase 0.25 mg/mL in dPBS at 25°C for 15 min followed by manual trituration with a flame polished glass pipette for 5 min. Cell suspensions were then filtered through a 70 μm Nylon cell strainer to obtain a single cell suspension. Liberated cells were re suspended in 1% BSA / 5% FBS in dPBS and DAPI 0.1 μg/mL 15 min before FACS purification. All plastic and glass surfaces of cell contact were coated with 1% BSA in dPBS before to use. Prior to sorting for fluorescence levels single cells were isolated by sequentially gating cells according to their SSC A vs. FSC A FSC H vs FSC W and SSC H vs SSC W profiles according to standard flow cytometry practices. Cells with high levels of DAPI staining were excluded as dead or damaged. Cells from wild type zebrafish were used as negative control to determine gates for detection of mCherry and GFP fluorescence and then cells from transgenic fish were purified according to these gates. All samples were kept on ice except during Liberase incubation and then sorted chilled. 10X genomics V1 protocol following manufacturer recommendations. Fish were maintained at 28.5C with 10 h : 14 h light:dark conditions. Larvae were reared with marine rotifers supplemented with Artemac Aquafauna followed by Artemia and flake food. Adults were maintained on Artemia and flake food. Fish stocks of Danio rerio: WTABb a derivative of inbred ABwp Tgtyrp1b:palm mCherrywp.rt11 Tgpnp4a:palmmCherrywp.rt10 cell type:pigment cells|treatment:Untreated GSM3741778 GSM3741778: Zebrafish fin pigment cells; Danio rerio; RNA Seq GSM3741778   1 10X genomics V1 protocol following manufacturer recommendations.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP194294     leucophore_S9_L003_R2_001.fastq.gz leucophore_S9_L004_R1_001.fastq.gz fastq fastq 424061944.0 10241510.0 GSM3741778 r1 0:26 1:57 A:119042142;C:89897538;G:98172861;T:116716009;N:233394 26 57     119042142 89897538 98172861 116716009 233394 SRX5771765 SRS4705624 SRA881136 GEO Parichy Lab, Biology, University of Washington 1 0.33934   0.07693   0.8742   0.51425   57   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-04-30 Multi-stage Multi-stage Fin Surface Structure
53593 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.       zebrafish fin regeneration zebrafish fin 1dpa   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                 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.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP265421   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   10978857897 7760934381 8557391299 10029401940 92336569 SRX8434172 SRS6745285 SRA1081627 Stowers Institute for Medical Research|Sanchez lab Stowers Institute for Medical Research 1 0.92629   0.12539   0.78589   0.5225   91   B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_droplet 10x   United States 2020-08-11 Adult Adult Fin Surface Structure
55221 55221 SRR10182211 SRX6902836 SRS5434733 SRP223244 PRJNA574059 Cellular diversity of the regenerating caudal fin GSE137971 Transcriptome Analysis single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies filtered through 40 µm cell strainers and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging alignment to zebrafish reference genome GRCz10 and feature counting based on Ensembl release 91 cellranger count.   pubmed:32851162   1dpa fin1 scRNA GSM4095395   source name:1dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:1 day post amputation 1dpa fin1 scRNA All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell. 1dpa caudal fin   We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility with system water temperature at 28.5˚C and a day night cycle controlled as 14 hr light/10 hr dark. strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:1 day post amputation GSM4095395 GSM4095395: 1dpa fin1 scRNA; Danio rerio; RNA Seq GSM4095395   1 We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics GEO Accession:GSM4095395 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP223244     1dpa1_S1_L002_R1_001.fastq.gz 1dpa1_S1_L002_R2_001.fastq.gz fastq fastq 3515690517.0 34808817.0 GSM4095395 r1 0:26 1:75 A:1021208515;C:750623954;G:773148636;T:968849435;N:1859977 26 75     1021208515 750623954 773148636 968849435 1859977 SRX6902836 SRS5434733 SRA968154 GEO Ting Wang, Genetics, Washington University St Louis 2 0.00195 0.91495 0.00089 0.10966 0.99699 0.84855 0.35643 0.59738 26 75 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-09-25 Adult Adult Fin Surface Structure
55222 55222 SRR10182210 SRX6902835 SRS5434732 SRP223244 PRJNA574059 Cellular diversity of the regenerating caudal fin GSE137971 Transcriptome Analysis single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies filtered through 40 µm cell strainers and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging alignment to zebrafish reference genome GRCz10 and feature counting based on Ensembl release 91 cellranger count.   pubmed:32851162   preinjury fin2 scRNA GSM4095394   source name:Preinjury caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury preinjury fin2 scRNA All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell. Preinjury caudal fin   We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility with system water temperature at 28.5˚C and a day night cycle controlled as 14 hr light/10 hr dark. strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury GSM4095394 GSM4095394: preinjury fin2 scRNA; Danio rerio; RNA Seq GSM4095394   1 We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics GEO Accession:GSM4095394 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP223244     samp2_S2_L002_R2_001.fastq.gz samp2_S2_L002_R1_001.fastq.gz fastq fastq 14313306001.0 141715901.0 GSM4095394 r1 0:26 1:75 A:4080921082;C:3121900376;G:3341495424;T:3761528384;N:7460735 26 75     4080921082 3121900376 3341495424 3761528384 7460735 SRX6902835 SRS5434732 SRA968154 GEO Ting Wang, Genetics, Washington University St Louis 2 0.0029 0.89943 0.00115 0.07948 0.99543 0.8714 0.29607 0.47916 26 75 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-09-25 Adult Adult Fin Surface Structure
55223 55223 SRR10182209 SRX6902834 SRS5434731 SRP223244 PRJNA574059 Cellular diversity of the regenerating caudal fin GSE137971 Transcriptome Analysis single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies filtered through 40 µm cell strainers and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging alignment to zebrafish reference genome GRCz10 and feature counting based on Ensembl release 91 cellranger count.   pubmed:32851162   preinjury fin1 scRNA GSM4095393   source name:Preinjury caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury preinjury fin1 scRNA All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell. Preinjury caudal fin   We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility with system water temperature at 28.5˚C and a day night cycle controlled as 14 hr light/10 hr dark. strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury GSM4095393 GSM4095393: preinjury fin1 scRNA; Danio rerio; RNA Seq GSM4095393   1 We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics GEO Accession:GSM4095393 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP223244     samp1_S1_L001_R1_001.fastq.gz samp1_S1_L001_R2_001.fastq.gz fastq fastq 14610147425.0 144654925.0 GSM4095393 r1 0:26 1:75 A:4066051353;C:3189039694;G:3388950081;T:3856651906;N:109454391 26 75     4066051353 3189039694 3388950081 3856651906 109454391 SRX6902834 SRS5434731 SRA968154 GEO Ting Wang, Genetics, Washington University St Louis 2 0.0024 0.87757 0.00072 0.08379 0.99504 0.85269 0.34276 0.52515 26 75 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-09-25 Adult Adult Fin Surface Structure
55224 55224 SRR10182216 SRX6902833 SRS5434730 SRP223244 PRJNA574059 Cellular diversity of the regenerating caudal fin GSE137971 Transcriptome Analysis single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies filtered through 40 µm cell strainers and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging alignment to zebrafish reference genome GRCz10 and feature counting based on Ensembl release 91 cellranger count.   pubmed:32851162   4dpa fin2 scRNA GSM4095400   source name:4dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:4 day post amputation 4dpa fin2 scRNA All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell. 4dpa caudal fin   We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility with system water temperature at 28.5˚C and a day night cycle controlled as 14 hr light/10 hr dark. strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:4 day post amputation GSM4095400 GSM4095400: 4dpa fin2 scRNA; Danio rerio; RNA Seq GSM4095400   1 We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics GEO Accession:GSM4095400 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP223244     4dpa2_S2_L002_R1_001.fastq.gz 4dpa2_S2_L002_R2_001.fastq.gz fastq fastq 12205232082.0 120843882.0 GSM4095400 r1 0:26 1:75 A:3462691218;C:2662402586;G:2782962664;T:3293833482;N:3342132 26 75     3462691218 2662402586 2782962664 3293833482 3342132 SRX6902833 SRS5434730 SRA968154 GEO Ting Wang, Genetics, Washington University St Louis 2 0.00216 0.90418 0.00058 0.09381 0.99488 0.82666 0.33993 0.51619 26 75 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-09-25 Adult Adult Fin Surface Structure
55225 55225 SRR10182215 SRX6902832 SRS5434729 SRP223244 PRJNA574059 Cellular diversity of the regenerating caudal fin GSE137971 Transcriptome Analysis single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies filtered through 40 µm cell strainers and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging alignment to zebrafish reference genome GRCz10 and feature counting based on Ensembl release 91 cellranger count.   pubmed:32851162   4dpa fin1 scRNA GSM4095399   source name:4dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:4 day post amputation 4dpa fin1 scRNA All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell. 4dpa caudal fin   We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility with system water temperature at 28.5˚C and a day night cycle controlled as 14 hr light/10 hr dark. strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:4 day post amputation GSM4095399 GSM4095399: 4dpa fin1 scRNA; Danio rerio; RNA Seq GSM4095399   1 We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics GEO Accession:GSM4095399 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP223244     4dpa1_S1_L001_R1_001.fastq.gz 4dpa1_S1_L001_R2_001.fastq.gz fastq fastq 14335848494.0 141939094.0 GSM4095399 r1 0:26 1:75 A:4028586492;C:3145713740;G:3334469278;T:3823390760;N:3688224 26 75     4028586492 3145713740 3334469278 3823390760 3688224 SRX6902832 SRS5434729 SRA968154 GEO Ting Wang, Genetics, Washington University St Louis 2 0.00214 0.90496 0.00068 0.10148 0.99494 0.82014 0.36363 0.54339 26 75 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-09-25 Adult Adult Fin Surface Structure
55226 55226 SRR10182214 SRX6902831 SRS5434728 SRP223244 PRJNA574059 Cellular diversity of the regenerating caudal fin GSE137971 Transcriptome Analysis single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies filtered through 40 µm cell strainers and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging alignment to zebrafish reference genome GRCz10 and feature counting based on Ensembl release 91 cellranger count.   pubmed:32851162   2dpa fin2 scRNA GSM4095398   source name:2dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:2 day post amputation 2dpa fin2 scRNA All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell. 2dpa caudal fin   We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility with system water temperature at 28.5˚C and a day night cycle controlled as 14 hr light/10 hr dark. strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:2 day post amputation GSM4095398 GSM4095398: 2dpa fin2 scRNA; Danio rerio; RNA Seq GSM4095398   1 We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics GEO Accession:GSM4095398 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP223244     2dpa2_S2_L002_R1_001.fastq.gz 2dpa2_S2_L002_R2_001.fastq.gz fastq fastq 14592805725.0 144483225.0 GSM4095398 r1 0:26 1:75 A:4087287462;C:3228369053;G:3401290297;T:3861324848;N:14534065 26 75     4087287462 3228369053 3401290297 3861324848 14534065 SRX6902831 SRS5434728 SRA968154 GEO Ting Wang, Genetics, Washington University St Louis 2 0.00231 0.91223 0.00055 0.08705 0.99452 0.82627 0.30769 0.5211 26 75 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-09-25 Adult Adult Fin Surface Structure
55227 55227 SRR10182213 SRX6902830 SRS5434727 SRP223244 PRJNA574059 Cellular diversity of the regenerating caudal fin GSE137971 Transcriptome Analysis single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies filtered through 40 µm cell strainers and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging alignment to zebrafish reference genome GRCz10 and feature counting based on Ensembl release 91 cellranger count.   pubmed:32851162   2dpa fin1 scRNA GSM4095397   source name:2dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:2 day post amputation 2dpa fin1 scRNA All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell. 2dpa caudal fin   We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility with system water temperature at 28.5˚C and a day night cycle controlled as 14 hr light/10 hr dark. strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:2 day post amputation GSM4095397 GSM4095397: 2dpa fin1 scRNA; Danio rerio; RNA Seq GSM4095397   1 We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics GEO Accession:GSM4095397 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP223244     2dpa1_S1_L001_R1_001.fastq.gz 2dpa1_S1_L001_R2_001.fastq.gz fastq fastq 15317979261.0 151663161.0 GSM4095397 r1 0:26 1:75 A:4303056842;C:3349998898;G:3533853775;T:4116083703;N:14986043 26 75     4303056842 3349998898 3533853775 4116083703 14986043 SRX6902830 SRS5434727 SRA968154 GEO Ting Wang, Genetics, Washington University St Louis 2 0.0022 0.9122 0.0006 0.09555 0.99504 0.82203 0.33222 0.52299 26 75 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-09-25 Adult Adult Fin Surface Structure
55228 55228 SRR10182212 SRX6902829 SRS5434726 SRP223244 PRJNA574059 Cellular diversity of the regenerating caudal fin GSE137971 Transcriptome Analysis single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies filtered through 40 µm cell strainers and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging alignment to zebrafish reference genome GRCz10 and feature counting based on Ensembl release 91 cellranger count.   pubmed:32851162   1dpa fin2 scRNA GSM4095396   source name:1dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:1 day post amputation 1dpa fin2 scRNA All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell. 1dpa caudal fin   We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility with system water temperature at 28.5˚C and a day night cycle controlled as 14 hr light/10 hr dark. strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:1 day post amputation GSM4095396 GSM4095396: 1dpa fin2 scRNA; Danio rerio; RNA Seq GSM4095396   1 We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics GEO Accession:GSM4095396 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP223244     1dpa2_S2_L002_R2_001.fastq.gz 1dpa2_S2_L002_R1_001.fastq.gz fastq fastq 10934230609.0 108259709.0 GSM4095396 r1 0:26 1:75 A:3111673507;C:2358969825;G:2438293271;T:3019487882;N:5806124 26 75     3111673507 2358969825 2438293271 3019487882 5806124 SRX6902829 SRS5434726 SRA968154 GEO Ting Wang, Genetics, Washington University St Louis 2 0.00198 0.92416 0.00054 0.08626 0.99596 0.83808 0.29818 0.52586 26 75 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-09-25 Adult Adult Fin Surface Structure
61429 61429 SRR12749699 SRX9221655 SRS7455356 SRP285950 PRJNA666695 Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae GSE158851 Transcriptome Analysis Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation. Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform and sequenced using Illumina NovaSeq 6000. Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets previously described by our group to govern zebrafish fin regeneration and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.   pubmed:34732706;pubmed:35664055   Uncut caudal fin scRNA GSM4812244   source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation Uncut caudal fin scRNA Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format : the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination ; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'. caudal fin   Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222 Sigma in zebrafish water. Approximately 150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer’s instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.   tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation GSM4812244 GSM4812244: Uncut caudal fin scRNA; Danio rerio; RNA Seq GSM4812244   1 Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222 Sigma in zebrafish water. Approximately 150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument. GEO Accession:GSM4812244 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP285950   loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=Uncut S8 L001 R1 001.fastq.gz read2PairFiles=Uncut S8 L001 R2 001.fastq.gz read3PairFiles=Uncut S8 L001 I1 001.fastq.gz Uncut_S8_L001_I1_001.fastq.gz Uncut_S8_L001_R1_001.fastq.gz Uncut_S8_L001_R2_001.fastq.gz fastq fastq fastq 18909629967.0 153736829.0 GSM4812244 r1 0:28 1:87 2:8 A:5220924848;C:4279280050;G:4788532540;T:4619612909;N:1279620 28 87 8   5220924848 4279280050 4788532540 4619612909 1279620 SRX9221655 SRS7455356 SRA1136463 GEO Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm 1 0.63376   0.11724   0.8393   0.55679   87   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   France 2020-09-30 Larval Larval Fin Surface Structure
61430 61430 SRR12749700 SRX9221655 SRS7455356 SRP285950 PRJNA666695 Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae GSE158851 Transcriptome Analysis Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation. Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform and sequenced using Illumina NovaSeq 6000. Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets previously described by our group to govern zebrafish fin regeneration and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.   pubmed:34732706;pubmed:35664055   Uncut caudal fin scRNA GSM4812244   source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation Uncut caudal fin scRNA Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format : the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination ; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'. caudal fin   Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222 Sigma in zebrafish water. Approximately 150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer’s instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.   tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation GSM4812244 GSM4812244: Uncut caudal fin scRNA; Danio rerio; RNA Seq GSM4812244   1 Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222 Sigma in zebrafish water. Approximately 150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument. GEO Accession:GSM4812244 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP285950   loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=Uncut S8 L002 R1 001.fastq.gz read2PairFiles=Uncut S8 L002 R2 001.fastq.gz read3PairFiles=Uncut S8 L002 I1 001.fastq.gz Uncut_S8_L002_I1_001.fastq.gz Uncut_S8_L002_R1_001.fastq.gz Uncut_S8_L002_R2_001.fastq.gz fastq fastq fastq 18967585107.0 154208009.0 GSM4812244 r2 0:28 1:87 2:8 A:5236542259;C:4292274179;G:4804216460;T:4633355352;N:1196857 28 87 8   5236542259 4292274179 4804216460 4633355352 1196857 SRX9221655 SRS7455356 SRA1136463 GEO Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm 1 0.63437   0.11726   0.83857   0.5661   87   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   France 2020-09-30 Larval Larval Fin Surface Structure
61431 61431 SRR12749697 SRX9221654 SRS7455355 SRP285950 PRJNA666695 Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae GSE158851 Transcriptome Analysis Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation. Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform and sequenced using Illumina NovaSeq 6000. Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets previously described by our group to govern zebrafish fin regeneration and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.   pubmed:34732706;pubmed:35664055   Cut caudal fin scRNA GSM4812243   source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours Cut caudal fin scRNA Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format : the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination ; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'. caudal fin   Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222 Sigma in zebrafish water. Approximately 150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer’s instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.   tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours GSM4812243 GSM4812243: Cut caudal fin scRNA; Danio rerio; RNA Seq GSM4812243   1 Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222 Sigma in zebrafish water. Approximately 150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument. GEO Accession:GSM4812243 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP285950   loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=Cut S7 L001 R1 001.fastq.gz read2PairFiles=Cut S7 L001 R2 001.fastq.gz read3PairFiles=Cut S7 L001 I1 001.fastq.gz Cut_S7_L001_I1_001.fastq.gz Cut_S7_L001_R1_001.fastq.gz Cut_S7_L001_R2_001.fastq.gz fastq fastq fastq 17453571711.0 141898957.0 GSM4812243 r1 0:28 1:87 2:8 A:4820960991;C:3908308491;G:4347557585;T:4375565175;N:1179469 28 87 8   4820960991 3908308491 4347557585 4375565175 1179469 SRX9221654 SRS7455355 SRA1136463 GEO Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm 1 0.63902   0.11232   0.82235   0.50797   87   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   France 2020-09-30 Larval Larval Fin Surface Structure
61432 61432 SRR12749698 SRX9221654 SRS7455355 SRP285950 PRJNA666695 Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae GSE158851 Transcriptome Analysis Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation. Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform and sequenced using Illumina NovaSeq 6000. Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets previously described by our group to govern zebrafish fin regeneration and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.   pubmed:34732706;pubmed:35664055   Cut caudal fin scRNA GSM4812243   source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours Cut caudal fin scRNA Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format : the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination ; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'. caudal fin   Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222 Sigma in zebrafish water. Approximately 150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer’s instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.   tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours GSM4812243 GSM4812243: Cut caudal fin scRNA; Danio rerio; RNA Seq GSM4812243   1 Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222 Sigma in zebrafish water. Approximately 150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument. GEO Accession:GSM4812243 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP285950   loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=Cut S7 L002 R1 001.fastq.gz read2PairFiles=Cut S7 L002 R2 001.fastq.gz read3PairFiles=Cut S7 L002 I1 001.fastq.gz Cut_S7_L002_I1_001.fastq.gz Cut_S7_L002_R1_001.fastq.gz Cut_S7_L002_R2_001.fastq.gz fastq fastq fastq 17511283926.0 142368162.0 GSM4812243 r2 0:28 1:87 2:8 A:4836849959;C:3920920286;G:4362769830;T:4389644044;N:1099807 28 87 8   4836849959 3920920286 4362769830 4389644044 1099807 SRX9221654 SRS7455355 SRA1136463 GEO Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm 1 0.63847   0.11249   0.82231   0.51524   87   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   France 2020-09-30 Larval Larval Fin Surface Structure
65589 65589 SRR15390211 SRX11692441 SRS9724035 SRP331755 PRJNA753151 scRNA seq of fin and body zebrafish melanocytes GSE181748 Transcriptome Analysis Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body whereas the acral subtype arises on the palms of the hands soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes compared to body melanocytes revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma which was generated by injecting Casper fish with MniCoopR GFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total GFP+ body cells GFP body cells GFP+ fin cells GFP fin cells. Data was then analyzed and pooled together …   pubmed:35355015   XFN GSM5510267   source name:Zebrafish fins|model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP XFN Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao Hao et al. 2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija 2019. Principal component analysis Joliffe 1986 and UMAP dimensionality reduction McInnes 2018 were performed using default parameters with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al. 2020; Hunter Moncada et al. 2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output Zebrafish fins   Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics   model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP GSM5510267 GSM5510267: XFN; Danio rerio; RNA Seq GSM5510267   1 Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics GEO Accession:GSM5510267 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP331755     2385_XFN_IGO_11718_4_S4_L001_R1_001.fastq.gz 2385_XFN_IGO_11718_4_S4_L001_R2_001.fastq.gz fastq fastq 20452607604.0 174808612.0 GSM5510267 r1 0:29 1:88 A:5729911089;C:4526353776;G:4631244451;T:5564405432;N:692856 29 88     5729911089 4526353776 4631244451 5564405432 692856 SRX11692441 SRS9724035 SRA1274997 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.00608 0.85139 0.00196 0.14282 0.99093 0.78543 0.42676 0.53168 29 88 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-09 Undetermined Adult Fin Surface Structure
65590 65590 SRR15390212 SRX11692441 SRS9724035 SRP331755 PRJNA753151 scRNA seq of fin and body zebrafish melanocytes GSE181748 Transcriptome Analysis Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body whereas the acral subtype arises on the palms of the hands soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes compared to body melanocytes revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma which was generated by injecting Casper fish with MniCoopR GFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total GFP+ body cells GFP body cells GFP+ fin cells GFP fin cells. Data was then analyzed and pooled together …   pubmed:35355015   XFN GSM5510267   source name:Zebrafish fins|model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP XFN Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao Hao et al. 2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija 2019. Principal component analysis Joliffe 1986 and UMAP dimensionality reduction McInnes 2018 were performed using default parameters with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al. 2020; Hunter Moncada et al. 2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output Zebrafish fins   Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics   model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP GSM5510267 GSM5510267: XFN; Danio rerio; RNA Seq GSM5510267   1 Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics GEO Accession:GSM5510267 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP331755     2385_XFN_IGO_11718_4_S4_L002_R1_001.fastq.gz 2385_XFN_IGO_11718_4_S4_L002_R2_001.fastq.gz fastq fastq 20056571028.0 171423684.0 GSM5510267 r2 0:29 1:88 A:5624358913;C:4435209829;G:4536840173;T:5459497012;N:665101 29 88     5624358913 4435209829 4536840173 5459497012 665101 SRX11692441 SRS9724035 SRA1274997 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.00636 0.85263 0.00229 0.14314 0.99113 0.78206 0.42564 0.53095 29 88 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-09 Undetermined Adult Fin Surface Structure
65591 65591 SRR15390209 SRX11692439 SRS9724039 SRP331755 PRJNA753151 scRNA seq of fin and body zebrafish melanocytes GSE181748 Transcriptome Analysis Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body whereas the acral subtype arises on the palms of the hands soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes compared to body melanocytes revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma which was generated by injecting Casper fish with MniCoopR GFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total GFP+ body cells GFP body cells GFP+ fin cells GFP fin cells. Data was then analyzed and pooled together …   pubmed:35355015   XFG GSM5510266   source name:Zebrafish fins|model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP+ XFG Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao Hao et al. 2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija 2019. Principal component analysis Joliffe 1986 and UMAP dimensionality reduction McInnes 2018 were performed using default parameters with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al. 2020; Hunter Moncada et al. 2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output Zebrafish fins   Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics   model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP+ GSM5510266 GSM5510266: XFG; Danio rerio; RNA Seq GSM5510266   1 Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics GEO Accession:GSM5510266 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP331755     2384_XFG_IGO_11718_3_S3_L001_R1_001.fastq.gz 2384_XFG_IGO_11718_3_S3_L001_R2_001.fastq.gz fastq fastq 21239736102.0 181536206.0 GSM5510266 r1 0:29 1:88 A:6013451435;C:4631285818;G:4786546365;T:5807740759;N:711725 29 88     6013451435 4631285818 4786546365 5807740759 711725 SRX11692439 SRS9724039 SRA1274997 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.00797 0.89811 0.00258 0.14942 0.9889 0.79259 0.38209 0.54357 29 88 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-09 Undetermined Adult Fin Surface Structure
65592 65592 SRR15390210 SRX11692439 SRS9724039 SRP331755 PRJNA753151 scRNA seq of fin and body zebrafish melanocytes GSE181748 Transcriptome Analysis Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body whereas the acral subtype arises on the palms of the hands soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes compared to body melanocytes revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma which was generated by injecting Casper fish with MniCoopR GFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total GFP+ body cells GFP body cells GFP+ fin cells GFP fin cells. Data was then analyzed and pooled together …   pubmed:35355015   XFG GSM5510266   source name:Zebrafish fins|model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP+ XFG Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao Hao et al. 2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija 2019. Principal component analysis Joliffe 1986 and UMAP dimensionality reduction McInnes 2018 were performed using default parameters with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al. 2020; Hunter Moncada et al. 2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output Zebrafish fins   Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics   model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP+ GSM5510266 GSM5510266: XFG; Danio rerio; RNA Seq GSM5510266   1 Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics GEO Accession:GSM5510266 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP331755     2384_XFG_IGO_11718_3_S3_L002_R1_001.fastq.gz 2384_XFG_IGO_11718_3_S3_L002_R2_001.fastq.gz fastq fastq 20799675234.0 177775002.0 GSM5510266 r2 0:29 1:88 A:5894902894;C:4531100030;G:4681582244;T:5691398362;N:691704 29 88     5894902894 4531100030 4681582244 5691398362 691704 SRX11692439 SRS9724039 SRA1274997 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.00787 0.89764 0.00227 0.14926 0.98821 0.78928 0.40092 0.53114 29 88 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-09 Undetermined Adult Fin Surface Structure
71755 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   pubmed:37290497   7 dpa scRNA seq GSM6670935   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   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 μm 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 3’ 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.   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 μm 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP404046   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   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   0.20943   0.79935   0.6085   101   B   usable mapping rate illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   United States 2022-10-22 Adult Adult Fin Surface Structure
71756 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   pubmed:37290497   7 dpa scRNA seq GSM6670935   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   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 μm 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 3’ 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.   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 μm 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP404046   loader:fastq load.py 3669_7dpa_S5_L002_I1_001.fastq.gz 3669_7dpa_S5_L002_R1_001.fastq.gz 3669_7dpa_S5_L002_R2_001.fastq.gz fastq fastq fastq 14699346911.0 107294503.0 GSM6670935 r2 0:8 1:28 2:101 A:3181472399;C:2279044984;G:2296050130;T:3077615290;N:2562000 8 28 101   3181472399 2279044984 2296050130 3077615290 2562000 SRX17995702 SRS15506856 SRA1525679 Stankunas, Institute of Molecular Biology, University of Oregon Stankunas, Institute of Molecular Biology, University of Oregon 1 0.89055   0.21159   0.80168   0.60887   101   B   usable mapping rate illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   United States 2022-10-22 Adult Adult Fin Surface Structure
71757 71757 SRR22013538 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   pubmed:37290497   3 dpa scRNA seq GSM6670934   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   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 μm 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 3’ 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.   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 μm 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'   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP404046   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   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   0.19536   0.78597   0.5661   101   B   usable mapping rate illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   United States 2022-10-22 Adult Adult Fin Surface Structure
71758 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   pubmed:37290497   3 dpa scRNA seq GSM6670934   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   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 μm 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 3’ 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.   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 μm 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'   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP404046   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   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   0.19517   0.78524   0.57129   101   B   usable mapping rate illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   United States 2022-10-22 Adult Adult Fin Surface Structure

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;