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29 rows where experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL", experiment.platform = "ILLUMINA" and tissue_curation = "Fin"

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devstage_curation_coarse 3

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tissue_curation_coarse 1

tissue_curation 1

  • Fin · 29 ✖

technology 1

experiment.platform 1

  • ILLUMINA · 29 ✖

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC SINGLE CELL · 29 ✖

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
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
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");;