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,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,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,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,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,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,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,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,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,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,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,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,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,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,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
31525,SRR28419473,SRX24023800,SRS20818155,SRP497235,PRJNA1090867,Single cell RNA seq of zebrafish endothelial cells,GSE262232,Transcriptome Analysis,We performed single cell RNA sequencing scRNA seq for isolated endothelial cells Overall design: Tgkdrl:EGFP zebrafish embryos were digested into single cell suspension  EGFP positive cells were isolated using FACS and subjected to 10X Genomics Chromium scRNAseq.,,pubmed:39977018,,Zebrafish endothelial cells 3 dpf 2,GSM8160887,,source name:Whole body|tissue:Whole body|age:embryo|geo loc name:missing|collection date:missing,Zebrafish endothelial cells 3 dpf 2,Cell Ranger v2.1 was used to de multiplex raw base call BCL files generated by Illumina sequencers into FASTQ files  perform the alignment  barcode counting  and UMI counting. Assembly: GRCz11 Supplementary files format and content: Tab seprated values files,Whole body,,Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions  EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM  Library and Gel Bead Kit v2 10X Genomics according to manufacturer’s protocol.,,tissue:Whole body|age:embryo,GSM8160887,GSM8160887: Zebrafish endothelial cells 3 dpf 2; Danio rerio; RNA Seq,GSM8160887 r1,GSM8160887,1,Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions  EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM  Library and Gel Bead Kit v2 10X Genomics according to manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP497235,,assembly:GRCz11|intentional duplicate|dangling references:treat as unmapped|dangling references:skip reference resolution,3dpf_2_possorted_genome_bam.bam,10X Genomics bam file,8478190406.0,86512147.0,GSM8160887 r1,0:98,A:2448546566;C:1819820402;G:2005413327;T:2187171703;N:17238408,98,,,,2448546566,1819820402,2005413327,2187171703,17238408,SRX24023800,SRS20818155,SRA1835509,Uppsala University,Uppsala University,1,0.91631,,0.11199,,0.82106,,0.54746,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-03-22,Larval,Larval,Trunk,Surface Structure
31526,SRR28419474,SRX24023799,SRS20818156,SRP497235,PRJNA1090867,Single cell RNA seq of zebrafish endothelial cells,GSE262232,Transcriptome Analysis,We performed single cell RNA sequencing scRNA seq for isolated endothelial cells Overall design: Tgkdrl:EGFP zebrafish embryos were digested into single cell suspension  EGFP positive cells were isolated using FACS and subjected to 10X Genomics Chromium scRNAseq.,,pubmed:39977018,,Zebrafish endothelial cells 3 dpf 1,GSM8160886,,source name:Whole body|tissue:Whole body|age:embryo|geo loc name:missing|collection date:missing,Zebrafish endothelial cells 3 dpf 1,Cell Ranger v2.1 was used to de multiplex raw base call BCL files generated by Illumina sequencers into FASTQ files  perform the alignment  barcode counting  and UMI counting. Assembly: GRCz11 Supplementary files format and content: Tab seprated values files,Whole body,,Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions  EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM  Library and Gel Bead Kit v2 10X Genomics according to manufacturer’s protocol.,,tissue:Whole body|age:embryo,GSM8160886,GSM8160886: Zebrafish endothelial cells 3 dpf 1; Danio rerio; RNA Seq,GSM8160886 r1,GSM8160886,1,Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions  EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM  Library and Gel Bead Kit v2 10X Genomics according to manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP497235,,assembly:GRCz11|intentional duplicate|dangling references:treat as unmapped|dangling references:skip reference resolution,3dpf_1_possorted_genome_bam.bam,10X Genomics bam file,2842123088.0,29001256.0,GSM8160886 r1,0:98,A:821846800;C:603425858;G:657525459;T:720690292;N:38634679,98,,,,821846800,603425858,657525459,720690292,38634679,SRX24023799,SRS20818156,SRA1835509,Uppsala University,Uppsala University,1,0.86292,,0.0954,,0.82844,,0.52761,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-03-22,Larval,Larval,Trunk,Surface Structure
31527,SRR28419475,SRX24023798,SRS20818154,SRP497235,PRJNA1090867,Single cell RNA seq of zebrafish endothelial cells,GSE262232,Transcriptome Analysis,We performed single cell RNA sequencing scRNA seq for isolated endothelial cells Overall design: Tgkdrl:EGFP zebrafish embryos were digested into single cell suspension  EGFP positive cells were isolated using FACS and subjected to 10X Genomics Chromium scRNAseq.,,pubmed:39977018,,Zebrafish endothelial cells 34 hpf,GSM8160885,,source name:Whole body|tissue:Whole body|age:embryo|geo loc name:missing|collection date:missing,Zebrafish endothelial cells 34 hpf,Cell Ranger v2.1 was used to de multiplex raw base call BCL files generated by Illumina sequencers into FASTQ files  perform the alignment  barcode counting  and UMI counting. Assembly: GRCz11 Supplementary files format and content: Tab seprated values files,Whole body,,Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions  EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM  Library and Gel Bead Kit v2 10X Genomics according to manufacturer’s protocol.,,tissue:Whole body|age:embryo,GSM8160885,GSM8160885: Zebrafish endothelial cells 34 hpf; Danio rerio; RNA Seq,GSM8160885 r1,GSM8160885,1,Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions  EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM  Library and Gel Bead Kit v2 10X Genomics according to manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP497235,,assembly:GRCz11|intentional duplicate|dangling references:treat as unmapped|dangling references:skip reference resolution,34hpf_possorted_genome_bam.bam,10X Genomics bam file,8518745844.0,86925978.0,GSM8160885 r1,0:98,A:2440648674;C:1828442217;G:2000096456;T:2232243146;N:17315351,98,,,,2440648674,1828442217,2000096456,2232243146,17315351,SRX24023798,SRS20818154,SRA1835509,Uppsala University,Uppsala University,1,0.92268,,0.1011,,0.82235,,0.50276,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-03-22,Pharyngula,Embryo,Trunk,Surface Structure
33892,SRR30866052,SRX26263961,SRS22803217,SRP536276,PRJNA1168147,Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [scRNA seq],GSE278654,Transcriptome Analysis,Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To understand how selective N glycosylation modification performed by mgat4b promote melanocyte development  we performed single cell RNA sequencing of mitfa+ve melanophores sorted from the 36hpf staged zebrafish.,,,,m4b mut,GSM8552316,,tissue:melanocytes|cell type:melanocytes|age:36 hpf|genotype:mgat4b mutant|treatment:No|geo loc name:missing|collection date:missing,m4b mut,Cellranger mkfastq pipeline was used to generate fastq files The fastq files were then aligned with custom zebrafish reference assembly GRCz11 using cellranger. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including barcodes and features  and matrix files,melanocytes,,The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction,,cell type:melanocytes|age:36 hpf|genotype:mgat4b mutant|treatment:No,GSM8552316,GSM8552316: m4b mut; Danio rerio; RNA Seq,GSM8552316 r1,GSM8552316,1,The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536276,,loader:fastq load.py,m4b_mut_S2_L001_I1_001.fastq.gz m4b_mut_S2_L001_I2_001.fastq.gz m4b_mut_S2_L001_R1_001.fastq.gz m4b_mut_S2_L001_R2_001.fastq.gz,fastq fastq fastq fastq,18274385040.0,132423080.0,GSM8552316 r1,0:10 1:10 2:28 3:90,A:3788703303;C:2355223955;G:2645521958;T:3126630009;N:1997975,10,10,28,90,3788703303,2355223955,2645521958,3126630009,1997975,SRX26263961,SRS22803217,SRA1984944,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,India,2024-10-02,Pharyngula,Embryo,Skin,Surface Structure
33893,SRR30866053,SRX26263960,SRS22803216,SRP536276,PRJNA1168147,Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [scRNA seq],GSE278654,Transcriptome Analysis,Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To understand how selective N glycosylation modification performed by mgat4b promote melanocyte development  we performed single cell RNA sequencing of mitfa+ve melanophores sorted from the 36hpf staged zebrafish.,,,,Control,GSM8552315,,tissue:melanocytes|cell type:melanocytes|age:36 hpf|genotype:control|treatment:No|geo loc name:missing|collection date:missing,Control,Cellranger mkfastq pipeline was used to generate fastq files The fastq files were then aligned with custom zebrafish reference assembly GRCz11 using cellranger. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including barcodes and features  and matrix files,melanocytes,,The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction,,cell type:melanocytes|age:36 hpf|genotype:control|treatment:No,GSM8552315,GSM8552315: Control; Danio rerio; RNA Seq,GSM8552315 r1,GSM8552315,1,The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536276,,loader:fastq load.py,con_S1_L001_I1_001.fastq.gz con_S1_L001_I2_001.fastq.gz con_S1_L001_R1_001.fastq.gz con_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,15825218034.0,114675493.0,GSM8552315 r1,0:10 1:10 2:28 3:90,A:3074750870;C:2137365424;G:2401965854;T:2704984993;N:1727229,10,10,28,90,3074750870,2137365424,2401965854,2704984993,1727229,SRX26263960,SRS22803216,SRA1984944,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,India,2024-10-02,Pharyngula,Embryo,Skin,Surface Structure
34143,SRR31364121,SRX26737888,SRS23227909,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “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,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,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,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,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,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,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,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,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,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
34294,SRR31642040,SRX27005496,SRS23470018,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  70 dpjr  Single,GSM8671781,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  70 dpjr  Single,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2,GSM8671781,GSM8671781: Jaw joint cells  70 dpjr  Single; Danio rerio; RNA Seq,GSM8671781 r1,GSM8671781,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,70dpjr_Single_Animal_L002_I1_001.fastq.gz 70dpjr_Single_Animal_L002_I2_001.fastq.gz 70dpjr_Single_Animal_L002_R1_001.fastq.gz 70dpjr_Single_Animal_L002_R2_001.fastq.gz,fastq fastq fastq fastq,37049181954.0,166888207.0,GSM8671781 r1,0:10 1:10 2:101 3:101,A:9816927833;C:6602658028;G:6479430305;T:10811804702;N:596946,10,10,101,101,9816927833,6602658028,6479430305,10811804702,596946,SRX27005496,SRS23470018,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34295,SRR31642041,SRX27005496,SRS23470018,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  70 dpjr  Single,GSM8671781,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  70 dpjr  Single,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2,GSM8671781,GSM8671781: Jaw joint cells  70 dpjr  Single; Danio rerio; RNA Seq,GSM8671781 r1,GSM8671781,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,70dpjr_Single_Animal_L003_I1_001.fastq.gz 70dpjr_Single_Animal_L003_I2_001.fastq.gz 70dpjr_Single_Animal_L003_R1_001.fastq.gz 70dpjr_Single_Animal_L003_R2_001.fastq.gz,fastq fastq fastq fastq,37422563532.0,168570106.0,GSM8671781 r2,0:10 1:10 2:101 3:101,A:9984119286;C:6706845163;G:6549173156;T:10810402697;N:621110,10,10,101,101,9984119286,6706845163,6549173156,10810402697,621110,SRX27005496,SRS23470018,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34296,SRR31642042,SRX27005495,SRS23470017,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  70 dpjr  Pooled,GSM8671780,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  70 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2,GSM8671780,GSM8671780: Jaw joint cells  70 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671780 r1,GSM8671780,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,70dpjr_Pooled_L002_I1_001.fastq.gz 70dpjr_Pooled_L002_I2_001.fastq.gz 70dpjr_Pooled_L002_R1_001.fastq.gz 70dpjr_Pooled_L002_R2_001.fastq.gz,fastq fastq fastq fastq,38777301438.0,174672529.0,GSM8671780 r1,0:10 1:10 2:101 3:101,A:10225368778;C:6854296513;G:6738650656;T:11464913181;N:621730,10,10,101,101,10225368778,6854296513,6738650656,11464913181,621730,SRX27005495,SRS23470017,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34297,SRR31642043,SRX27005495,SRS23470017,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  70 dpjr  Pooled,GSM8671780,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  70 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2,GSM8671780,GSM8671780: Jaw joint cells  70 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671780 r1,GSM8671780,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,70dpjr_Pooled_L003_I1_001.fastq.gz 70dpjr_Pooled_L003_I2_001.fastq.gz 70dpjr_Pooled_L003_R1_001.fastq.gz 70dpjr_Pooled_L003_R2_001.fastq.gz,fastq fastq fastq fastq,39504660018.0,177948919.0,GSM8671780 r2,0:10 1:10 2:101 3:101,A:10484112013;C:7025634996;G:6867358428;T:11567917628;N:658573,10,10,101,101,10484112013,7025634996,6867358428,11567917628,658573,SRX27005495,SRS23470017,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34298,SRR31642044,SRX27005494,SRS23470016,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  28 dpjr  Single Animal,GSM8671779,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  28 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2,GSM8671779,GSM8671779: Jaw joint cells  28 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671779 r1,GSM8671779,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,28dpjr_Single_Animal_L002_I1_001.fastq.gz 28dpjr_Single_Animal_L002_I2_001.fastq.gz 28dpjr_Single_Animal_L002_R1_001.fastq.gz 28dpjr_Single_Animal_L002_R2_001.fastq.gz,fastq fastq fastq fastq,36462195750.0,164244125.0,GSM8671779 r1,0:10 1:10 2:101 3:101,A:9480759740;C:6602174265;G:6480198740;T:10613598349;N:582156,10,10,101,101,9480759740,6602174265,6480198740,10613598349,582156,SRX27005494,SRS23470016,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34299,SRR31642045,SRX27005494,SRS23470016,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  28 dpjr  Single Animal,GSM8671779,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  28 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2,GSM8671779,GSM8671779: Jaw joint cells  28 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671779 r1,GSM8671779,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,28dpjr_Single_Animal_L003_I1_001.fastq.gz 28dpjr_Single_Animal_L003_I2_001.fastq.gz 28dpjr_Single_Animal_L003_R1_001.fastq.gz 28dpjr_Single_Animal_L003_R2_001.fastq.gz,fastq fastq fastq fastq,37308768774.0,168057517.0,GSM8671779 r2,0:10 1:10 2:101 3:101,A:9765937139;C:6796393106;G:6628239898;T:10756427871;N:620420,10,10,101,101,9765937139,6796393106,6628239898,10756427871,620420,SRX27005494,SRS23470016,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34300,SRR31642046,SRX27005493,SRS23470015,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  28 dpjr  Pooled,GSM8671778,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  28 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2,GSM8671778,GSM8671778: Jaw joint cells  28 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671778 r1,GSM8671778,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,28dpjr_Pooled_L002_I1_001.fastq.gz 28dpjr_Pooled_L002_I2_001.fastq.gz 28dpjr_Pooled_L002_R1_001.fastq.gz 28dpjr_Pooled_L002_R2_001.fastq.gz,fastq fastq fastq fastq,37406314908.0,168496914.0,GSM8671778 r1,0:10 1:10 2:101 3:101,A:9851624515;C:6742015789;G:6561704544;T:10880437218;N:594562,10,10,101,101,9851624515,6742015789,6561704544,10880437218,594562,SRX27005493,SRS23470015,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34301,SRR31642047,SRX27005493,SRS23470015,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  28 dpjr  Pooled,GSM8671778,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  28 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2,GSM8671778,GSM8671778: Jaw joint cells  28 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671778 r1,GSM8671778,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,28dpjr_Pooled_L003_I1_001.fastq.gz 28dpjr_Pooled_L003_I2_001.fastq.gz 28dpjr_Pooled_L003_R1_001.fastq.gz 28dpjr_Pooled_L003_R2_001.fastq.gz,fastq fastq fastq fastq,38288256750.0,172469625.0,GSM8671778 r2,0:10 1:10 2:101 3:101,A:10150332803;C:6940223173;G:6717128076;T:11030541750;N:638448,10,10,101,101,10150332803,6940223173,6717128076,11030541750,638448,SRX27005493,SRS23470015,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34302,SRR31642048,SRX27005492,SRS23470014,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  14 dpjr  Single Animal,GSM8671777,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:14 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  14 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:14 dpjr|batch:2,GSM8671777,GSM8671777: Jaw joint cells  14 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671777 r1,GSM8671777,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,14dpjr_Single_Animal_L002_I1_001.fastq.gz 14dpjr_Single_Animal_L002_I2_001.fastq.gz 14dpjr_Single_Animal_L002_R1_001.fastq.gz 14dpjr_Single_Animal_L002_R2_001.fastq.gz,fastq fastq fastq fastq,37035287196.0,166825618.0,GSM8671777 r1,0:10 1:10 2:101 3:101,A:9648639338;C:6931863960;G:6677103016;T:10440574408;N:594114,10,10,101,101,9648639338,6931863960,6677103016,10440574408,594114,SRX27005492,SRS23470014,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34303,SRR31642049,SRX27005492,SRS23470014,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  14 dpjr  Single Animal,GSM8671777,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:14 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  14 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:14 dpjr|batch:2,GSM8671777,GSM8671777: Jaw joint cells  14 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671777 r1,GSM8671777,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,14dpjr_Single_Animal_L003_I1_001.fastq.gz 14dpjr_Single_Animal_L003_I2_001.fastq.gz 14dpjr_Single_Animal_L003_R1_001.fastq.gz 14dpjr_Single_Animal_L003_R2_001.fastq.gz,fastq fastq fastq fastq,37643417790.0,169564945.0,GSM8671777 r2,0:10 1:10 2:101 3:101,A:9871564441;C:7084478503;G:6791319850;T:10504128919;N:627177,10,10,101,101,9871564441,7084478503,6791319850,10504128919,627177,SRX27005492,SRS23470014,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34304,SRR31642050,SRX27005491,SRS23470013,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  14 dpjr  Pooled,GSM8671776,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:14 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  14 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:14 dpjr|batch:2,GSM8671776,GSM8671776: Jaw joint cells  14 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671776 r1,GSM8671776,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,14dpjr_Pooled_L002_I1_001.fastq.gz 14dpjr_Pooled_L002_I2_001.fastq.gz 14dpjr_Pooled_L002_R1_001.fastq.gz 14dpjr_Pooled_L002_R2_001.fastq.gz,fastq fastq fastq fastq,36987619800.0,166610900.0,GSM8671776 r1,0:10 1:10 2:101 3:101,A:9731052223;C:6612084734;G:6474066275;T:10837609042;N:589526,10,10,101,101,9731052223,6612084734,6474066275,10837609042,589526,SRX27005491,SRS23470013,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34305,SRR31642051,SRX27005491,SRS23470013,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  14 dpjr  Pooled,GSM8671776,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:14 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  14 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:14 dpjr|batch:2,GSM8671776,GSM8671776: Jaw joint cells  14 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671776 r1,GSM8671776,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,14dpjr_Pooled_L003_I1_001.fastq.gz 14dpjr_Pooled_L003_I2_001.fastq.gz 14dpjr_Pooled_L003_R1_001.fastq.gz 14dpjr_Pooled_L003_R2_001.fastq.gz,fastq fastq fastq fastq,37823124792.0,170374436.0,GSM8671776 r2,0:10 1:10 2:101 3:101,A:10018290148;C:6801679608;G:6619700517;T:10975336592;N:629207,10,10,101,101,10018290148,6801679608,6619700517,10975336592,629207,SRX27005491,SRS23470013,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34306,SRR31642052,SRX27005490,SRS23470012,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  7 dpjr  Single Animal,GSM8671775,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  7 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1,GSM8671775,GSM8671775: Jaw joint cells  7 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671775 r1,GSM8671775,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,7dpjr_Single_Animal_L001_I1_001.fastq.gz 7dpjr_Single_Animal_L001_I2_001.fastq.gz 7dpjr_Single_Animal_L001_R1_001.fastq.gz 7dpjr_Single_Animal_L001_R2_001.fastq.gz,fastq fastq fastq fastq,40902096516.0,184243678.0,GSM8671775 r1,0:10 1:10 2:101 3:101,A:9783975092;C:6823114397;G:6613251892;T:13996577499;N:304076,10,10,101,101,9783975092,6823114397,6613251892,13996577499,304076,SRX27005490,SRS23470012,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34307,SRR31642053,SRX27005490,SRS23470012,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  7 dpjr  Single Animal,GSM8671775,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  7 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1,GSM8671775,GSM8671775: Jaw joint cells  7 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671775 r1,GSM8671775,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,7dpjr_Single_Animal_L002_I1_001.fastq.gz 7dpjr_Single_Animal_L002_I2_001.fastq.gz 7dpjr_Single_Animal_L002_R1_001.fastq.gz 7dpjr_Single_Animal_L002_R2_001.fastq.gz,fastq fastq fastq fastq,41355254682.0,186284931.0,GSM8671775 r2,0:10 1:10 2:101 3:101,A:9943607268;C:6874125553;G:6628853095;T:14182629385;N:340761,10,10,101,101,9943607268,6874125553,6628853095,14182629385,340761,SRX27005490,SRS23470012,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34308,SRR31642054,SRX27005489,SRS23470011,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  7 dpjr  Pooled,GSM8671774,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  7 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1,GSM8671774,GSM8671774: Jaw joint cells  7 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671774 r1,GSM8671774,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,7dpjr_Pooled_L001_I1_001.fastq.gz 7dpjr_Pooled_L001_I2_001.fastq.gz 7dpjr_Pooled_L001_R1_001.fastq.gz 7dpjr_Pooled_L001_R2_001.fastq.gz,fastq fastq fastq fastq,53197411338.0,239627979.0,GSM8671774 r1,0:10 1:10 2:101 3:101,A:12697683552;C:8693291955;G:8466190901;T:18547291431;N:393919,10,10,101,101,12697683552,8693291955,8466190901,18547291431,393919,SRX27005489,SRS23470011,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34309,SRR31642055,SRX27005489,SRS23470011,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  7 dpjr  Pooled,GSM8671774,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  7 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1,GSM8671774,GSM8671774: Jaw joint cells  7 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671774 r1,GSM8671774,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,7dpjr_Pooled_L002_I1_001.fastq.gz 7dpjr_Pooled_L002_I2_001.fastq.gz 7dpjr_Pooled_L002_R1_001.fastq.gz 7dpjr_Pooled_L002_R2_001.fastq.gz,fastq fastq fastq fastq,53485697430.0,240926565.0,GSM8671774 r2,0:10 1:10 2:101 3:101,A:12829769456;C:8708244775;G:8441746450;T:18686966286;N:439163,10,10,101,101,12829769456,8708244775,8441746450,18686966286,439163,SRX27005489,SRS23470011,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34310,SRR31642056,SRX27005488,SRS23470010,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  3 dpjr  Single Animal,GSM8671773,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  3 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1,GSM8671773,GSM8671773: Jaw joint cells  3 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671773 r1,GSM8671773,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,3dpjr_Single_Animal_L001_I1_001.fastq.gz 3dpjr_Single_Animal_L001_I2_001.fastq.gz 3dpjr_Single_Animal_L001_R1_001.fastq.gz 3dpjr_Single_Animal_L001_R2_001.fastq.gz,fastq fastq fastq fastq,49273120002.0,221950991.0,GSM8671773 r1,0:10 1:10 2:101 3:101,A:11736989822;C:8276159891;G:8014521470;T:16806059958;N:369041,10,10,101,101,11736989822,8276159891,8014521470,16806059958,369041,SRX27005488,SRS23470010,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34311,SRR31642057,SRX27005488,SRS23470010,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  3 dpjr  Single Animal,GSM8671773,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  3 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1,GSM8671773,GSM8671773: Jaw joint cells  3 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671773 r1,GSM8671773,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,3dpjr_Single_Animal_L002_I1_001.fastq.gz 3dpjr_Single_Animal_L002_I2_001.fastq.gz 3dpjr_Single_Animal_L002_R1_001.fastq.gz 3dpjr_Single_Animal_L002_R2_001.fastq.gz,fastq fastq fastq fastq,49592342904.0,223388932.0,GSM8671773 r2,0:10 1:10 2:101 3:101,A:11873700952;C:8297783357;G:7995460477;T:16957208840;N:410638,10,10,101,101,11873700952,8297783357,7995460477,16957208840,410638,SRX27005488,SRS23470010,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34312,SRR31642058,SRX27005487,SRS23470009,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  3 dpjr  Pooled,GSM8671772,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  3 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1,GSM8671772,GSM8671772: Jaw joint cells  3 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671772 r1,GSM8671772,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,3dpjr_Pooled_L001_I1_001.fastq.gz 3dpjr_Pooled_L001_I2_001.fastq.gz 3dpjr_Pooled_L001_R1_001.fastq.gz 3dpjr_Pooled_L001_R2_001.fastq.gz,fastq fastq fastq fastq,44552263362.0,200685871.0,GSM8671772 r1,0:10 1:10 2:101 3:101,A:10490408187;C:7710053398;G:7420808306;T:14916942634;N:333417,10,10,101,101,10490408187,7710053398,7420808306,14916942634,333417,SRX27005487,SRS23470009,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34313,SRR31642059,SRX27005487,SRS23470009,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  3 dpjr  Pooled,GSM8671772,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  3 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1,GSM8671772,GSM8671772: Jaw joint cells  3 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671772 r1,GSM8671772,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,3dpjr_Pooled_L002_I1_001.fastq.gz 3dpjr_Pooled_L002_I2_001.fastq.gz 3dpjr_Pooled_L002_R1_001.fastq.gz 3dpjr_Pooled_L002_R2_001.fastq.gz,fastq fastq fastq fastq,44828540142.0,201930361.0,GSM8671772 r2,0:10 1:10 2:101 3:101,A:10609297758;C:7728774755;G:7401748035;T:15049741661;N:370713,10,10,101,101,10609297758,7728774755,7401748035,15049741661,370713,SRX27005487,SRS23470009,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34314,SRR31642060,SRX27005486,SRS23470008,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  1 dpjr  Single Animal,GSM8671771,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  1 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1,GSM8671771,GSM8671771: Jaw joint cells  1 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671771 r1,GSM8671771,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,1dpjr_Single_Animal_L001_I1_001.fastq.gz 1dpjr_Single_Animal_L001_I2_001.fastq.gz 1dpjr_Single_Animal_L001_R1_001.fastq.gz 1dpjr_Single_Animal_L001_R2_001.fastq.gz,fastq fastq fastq fastq,42674862642.0,192229111.0,GSM8671771 r1,0:10 1:10 2:101 3:101,A:10158179078;C:7131592111;G:6936536781;T:14603653251;N:319201,10,10,101,101,10158179078,7131592111,6936536781,14603653251,319201,SRX27005486,SRS23470008,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34315,SRR31642061,SRX27005486,SRS23470008,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  1 dpjr  Single Animal,GSM8671771,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  1 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1,GSM8671771,GSM8671771: Jaw joint cells  1 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671771 r1,GSM8671771,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,1dpjr_Single_Animal_L002_I1_001.fastq.gz 1dpjr_Single_Animal_L002_I2_001.fastq.gz 1dpjr_Single_Animal_L002_R1_001.fastq.gz 1dpjr_Single_Animal_L002_R2_001.fastq.gz,fastq fastq fastq fastq,42871754220.0,193116010.0,GSM8671771 r2,0:10 1:10 2:101 3:101,A:10257131897;C:7136718897;G:6908261223;T:14706965739;N:356264,10,10,101,101,10257131897,7136718897,6908261223,14706965739,356264,SRX27005486,SRS23470008,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34316,SRR31642062,SRX27005485,SRS23470007,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  1 dpjr  Pooled,GSM8671770,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  1 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1,GSM8671770,GSM8671770: Jaw joint cells  1 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671770 r1,GSM8671770,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,1dpjr_Pooled_L001_I1_001.fastq.gz 1dpjr_Pooled_L001_I2_001.fastq.gz 1dpjr_Pooled_L001_R1_001.fastq.gz 1dpjr_Pooled_L001_R2_001.fastq.gz,fastq fastq fastq fastq,42118392336.0,189722488.0,GSM8671770 r1,0:10 1:10 2:101 3:101,A:10107137753;C:6968180312;G:6833097097;T:14415214595;N:312819,10,10,101,101,10107137753,6968180312,6833097097,14415214595,312819,SRX27005485,SRS23470007,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34317,SRR31642063,SRX27005485,SRS23470007,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  1 dpjr  Pooled,GSM8671770,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  1 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1,GSM8671770,GSM8671770: Jaw joint cells  1 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671770 r1,GSM8671770,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,1dpjr_Pooled_L002_I1_001.fastq.gz 1dpjr_Pooled_L002_I2_001.fastq.gz 1dpjr_Pooled_L002_R1_001.fastq.gz 1dpjr_Pooled_L002_R2_001.fastq.gz,fastq fastq fastq fastq,42373992258.0,190873839.0,GSM8671770 r2,0:10 1:10 2:101 3:101,A:10221244303;C:6981947133;G:6814497183;T:14538473757;N:353102,10,10,101,101,10221244303,6981947133,6814497183,14538473757,353102,SRX27005485,SRS23470007,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34318,SRR31642064,SRX27005484,SRS23470006,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  Uninjured  Single Animal 2,GSM8671769,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  Uninjured  Single Animal 2,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:2,GSM8671769,GSM8671769: Jaw joint cells  Uninjured  Single Animal 2; Danio rerio; RNA Seq,GSM8671769 r1,GSM8671769,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,Uninjured_Single_Animal_2_L001_I1_001.fastq.gz Uninjured_Single_Animal_2_L001_I2_001.fastq.gz Uninjured_Single_Animal_2_L001_R1_001.fastq.gz Uninjured_Single_Animal_2_L001_R2_001.fastq.gz,fastq fastq fastq fastq,44002559172.0,198209726.0,GSM8671769 r1,0:10 1:10 2:101 3:101,A:10399936361;C:7407718592;G:7226570159;T:15003813457;N:326083,10,10,101,101,10399936361,7407718592,7226570159,15003813457,326083,SRX27005484,SRS23470006,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34319,SRR31642065,SRX27005484,SRS23470006,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  Uninjured  Single Animal 2,GSM8671769,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  Uninjured  Single Animal 2,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:2,GSM8671769,GSM8671769: Jaw joint cells  Uninjured  Single Animal 2; Danio rerio; RNA Seq,GSM8671769 r1,GSM8671769,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,Uninjured_Single_Animal_2_L002_I1_001.fastq.gz Uninjured_Single_Animal_2_L002_I2_001.fastq.gz Uninjured_Single_Animal_2_L002_R1_001.fastq.gz Uninjured_Single_Animal_2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,44326343508.0,199668214.0,GSM8671769 r2,0:10 1:10 2:101 3:101,A:10528879457;C:7433951690;G:7216222556;T:15153558176;N:367349,10,10,101,101,10528879457,7433951690,7216222556,15153558176,367349,SRX27005484,SRS23470006,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34320,SRR31642066,SRX27005483,SRS23470005,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  Uninjured  Single Animal 1,GSM8671768,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  Uninjured  Single Animal 1,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:1,GSM8671768,GSM8671768: Jaw joint cells  Uninjured  Single Animal 1; Danio rerio; RNA Seq,GSM8671768 r1,GSM8671768,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,Uninjured_Single_Animal_1_L002_I1_001.fastq.gz Uninjured_Single_Animal_1_L002_I2_001.fastq.gz Uninjured_Single_Animal_1_L002_R1_001.fastq.gz Uninjured_Single_Animal_1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,42273543918.0,190421369.0,GSM8671768 r1,0:10 1:10 2:101 3:101,A:10987118484;C:7700883520;G:7585109100;T:12191335494;N:669940,10,10,101,101,10987118484,7700883520,7585109100,12191335494,669940,SRX27005483,SRS23470005,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34321,SRR31642067,SRX27005483,SRS23470005,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  Uninjured  Single Animal 1,GSM8671768,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  Uninjured  Single Animal 1,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:1,GSM8671768,GSM8671768: Jaw joint cells  Uninjured  Single Animal 1; Danio rerio; RNA Seq,GSM8671768 r1,GSM8671768,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,Uninjured_Single_Animal_1_L003_I1_001.fastq.gz Uninjured_Single_Animal_1_L003_I2_001.fastq.gz Uninjured_Single_Animal_1_L003_R1_001.fastq.gz Uninjured_Single_Animal_1_L003_R2_001.fastq.gz,fastq fastq fastq fastq,43210917384.0,194643772.0,GSM8671768 r2,0:10 1:10 2:101 3:101,A:11303072754;C:7914534277;G:7759329632;T:12340392808;N:712473,10,10,101,101,11303072754,7914534277,7759329632,12340392808,712473,SRX27005483,SRS23470005,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34322,SRR31642068,SRX27005482,SRS23470004,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  Uninjured  Pooled,GSM8671767,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  Uninjured  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:2,GSM8671767,GSM8671767: Jaw joint cells  Uninjured  Pooled; Danio rerio; RNA Seq,GSM8671767 r1,GSM8671767,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,Uninjured_Pooled_L001_I1_001.fastq.gz Uninjured_Pooled_L001_I2_001.fastq.gz Uninjured_Pooled_L001_R1_001.fastq.gz Uninjured_Pooled_L001_R2_001.fastq.gz,fastq fastq fastq fastq,44953034856.0,202491148.0,GSM8671767 r1,0:10 1:10 2:101 3:101,A:10830949570;C:7341800999;G:7101623323;T:15628500376;N:337628,10,10,101,101,10830949570,7341800999,7101623323,15628500376,337628,SRX27005482,SRS23470004,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34323,SRR31642069,SRX27005482,SRS23470004,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  Uninjured  Pooled,GSM8671767,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  Uninjured  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:2,GSM8671767,GSM8671767: Jaw joint cells  Uninjured  Pooled; Danio rerio; RNA Seq,GSM8671767 r1,GSM8671767,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,Uninjured_Pooled_L002_I1_001.fastq.gz Uninjured_Pooled_L002_I2_001.fastq.gz Uninjured_Pooled_L002_R1_001.fastq.gz Uninjured_Pooled_L002_R2_001.fastq.gz,fastq fastq fastq fastq,45169152966.0,203464653.0,GSM8671767 r2,0:10 1:10 2:101 3:101,A:10937981456;C:7348369082;G:7073920761;T:15739215927;N:372680,10,10,101,101,10937981456,7348369082,7073920761,15739215927,372680,SRX27005482,SRS23470004,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34500,SRR31853995,SRX27213775,SRS23662882,SRP554457,PRJNA1204318,Spatially structured inflammatory response in the presence of a uniform stimulus: RNAseq screen,GSE285534,Transcriptome Analysis,Inflammatory responses occur within the complex spatial context of tissues and organs  and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here  we used single cell RNA sequencing to screen for genes differentially expressed under LPS lipopolysaccharide and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis. Overall design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS P. Aeuruginosa  Sigma  or E3 alone vehicle control  for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification.,,,,Control 10hr,GSM8703960,,source name:Body|tissue:Body|genotype:AB|age:6 dpf|treatment:control|geo loc name:missing|collection date:missing,Control 10hr,Sequencing data was aligned to the zebrafish reference genome GRCz11 using 10X Genomics Cellranger software 6.1.2. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Body,,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,tissue:Body|genotype:AB|age:6 dpf|treatment:control,GSM8703960,GSM8703960: Control 10hr; Danio rerio; RNA Seq,GSM8703960 r1,GSM8703960,1,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP554457,,loader:fastq load.py,Control_S12_L001_I1_001.fastq.gz Control_S12_L001_R1_001.fastq.gz Control_S12_L001_R2_001.fastq.gz,fastq fastq fastq,54727297835.0,430923605.0,GSM8703960 r1,0:8 1:28 2:91,A:11073804966;C:8703587106;G:9746134722;T:9686959402;N:3561859,8,28,91,,11073804966,8703587106,9746134722,9686959402,3561859,SRX27213775,SRS23662882,SRA2042619,"Jerison, Physics, University of Chicago","Jerison, Physics, University of Chicago",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-30,Larval,Larval,Trunk,Surface Structure
34501,SRR31853996,SRX27213775,SRS23662882,SRP554457,PRJNA1204318,Spatially structured inflammatory response in the presence of a uniform stimulus: RNAseq screen,GSE285534,Transcriptome Analysis,Inflammatory responses occur within the complex spatial context of tissues and organs  and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here  we used single cell RNA sequencing to screen for genes differentially expressed under LPS lipopolysaccharide and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis. Overall design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS P. Aeuruginosa  Sigma  or E3 alone vehicle control  for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification.,,,,Control 10hr,GSM8703960,,source name:Body|tissue:Body|genotype:AB|age:6 dpf|treatment:control|geo loc name:missing|collection date:missing,Control 10hr,Sequencing data was aligned to the zebrafish reference genome GRCz11 using 10X Genomics Cellranger software 6.1.2. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Body,,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,tissue:Body|genotype:AB|age:6 dpf|treatment:control,GSM8703960,GSM8703960: Control 10hr; Danio rerio; RNA Seq,GSM8703960 r1,GSM8703960,1,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP554457,,loader:fastq load.py,Control_S12_L002_I1_001.fastq.gz Control_S12_L002_R1_001.fastq.gz Control_S12_L002_R2_001.fastq.gz,fastq fastq fastq,55269352123.0,435191749.0,GSM8703960 r2,0:8 1:28 2:91,A:11174489058;C:8794319355;G:9857401155;T:9771712847;N:4526744,8,28,91,,11174489058,8794319355,9857401155,9771712847,4526744,SRX27213775,SRS23662882,SRA2042619,"Jerison, Physics, University of Chicago","Jerison, Physics, University of Chicago",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-30,Larval,Larval,Trunk,Surface Structure
34502,SRR31853997,SRX27213775,SRS23662882,SRP554457,PRJNA1204318,Spatially structured inflammatory response in the presence of a uniform stimulus: RNAseq screen,GSE285534,Transcriptome Analysis,Inflammatory responses occur within the complex spatial context of tissues and organs  and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here  we used single cell RNA sequencing to screen for genes differentially expressed under LPS lipopolysaccharide and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis. Overall design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS P. Aeuruginosa  Sigma  or E3 alone vehicle control  for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification.,,,,Control 10hr,GSM8703960,,source name:Body|tissue:Body|genotype:AB|age:6 dpf|treatment:control|geo loc name:missing|collection date:missing,Control 10hr,Sequencing data was aligned to the zebrafish reference genome GRCz11 using 10X Genomics Cellranger software 6.1.2. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Body,,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,tissue:Body|genotype:AB|age:6 dpf|treatment:control,GSM8703960,GSM8703960: Control 10hr; Danio rerio; RNA Seq,GSM8703960 r1,GSM8703960,1,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP554457,,loader:fastq load.py,Control_S12_L003_I1_001.fastq.gz Control_S12_L003_R1_001.fastq.gz Control_S12_L003_R2_001.fastq.gz,fastq fastq fastq,56713746491.0,446564933.0,GSM8703960 r3,0:8 1:28 2:91,A:11445709349;C:9041805308;G:10134400820;T:10010485583;N:5007843,8,28,91,,11445709349,9041805308,10134400820,10010485583,5007843,SRX27213775,SRS23662882,SRA2042619,"Jerison, Physics, University of Chicago","Jerison, Physics, University of Chicago",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-30,Larval,Larval,Trunk,Surface Structure
34503,SRR31853998,SRX27213775,SRS23662882,SRP554457,PRJNA1204318,Spatially structured inflammatory response in the presence of a uniform stimulus: RNAseq screen,GSE285534,Transcriptome Analysis,Inflammatory responses occur within the complex spatial context of tissues and organs  and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here  we used single cell RNA sequencing to screen for genes differentially expressed under LPS lipopolysaccharide and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis. Overall design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS P. Aeuruginosa  Sigma  or E3 alone vehicle control  for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification.,,,,Control 10hr,GSM8703960,,source name:Body|tissue:Body|genotype:AB|age:6 dpf|treatment:control|geo loc name:missing|collection date:missing,Control 10hr,Sequencing data was aligned to the zebrafish reference genome GRCz11 using 10X Genomics Cellranger software 6.1.2. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Body,,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,tissue:Body|genotype:AB|age:6 dpf|treatment:control,GSM8703960,GSM8703960: Control 10hr; Danio rerio; RNA Seq,GSM8703960 r1,GSM8703960,1,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP554457,,loader:fastq load.py,Control_S12_L004_I1_001.fastq.gz Control_S12_L004_R1_001.fastq.gz Control_S12_L004_R2_001.fastq.gz,fastq fastq fastq,55438180589.0,436521107.0,GSM8703960 r4,0:8 1:28 2:91,A:11203472019;C:8826429348;G:9895249162;T:9793520783;N:4749425,8,28,91,,11203472019,8826429348,9895249162,9793520783,4749425,SRX27213775,SRS23662882,SRA2042619,"Jerison, Physics, University of Chicago","Jerison, Physics, University of Chicago",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-30,Larval,Larval,Trunk,Surface Structure
34504,SRR31853999,SRX27213774,SRS23662881,SRP554457,PRJNA1204318,Spatially structured inflammatory response in the presence of a uniform stimulus: RNAseq screen,GSE285534,Transcriptome Analysis,Inflammatory responses occur within the complex spatial context of tissues and organs  and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here  we used single cell RNA sequencing to screen for genes differentially expressed under LPS lipopolysaccharide and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis. Overall design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS P. Aeuruginosa  Sigma  or E3 alone vehicle control  for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification.,,,,LPS 10hr,GSM8703959,,source name:Body|tissue:Body|genotype:AB|age:6 dpf|treatment:LPS|geo loc name:missing|collection date:missing,LPS 10hr,Sequencing data was aligned to the zebrafish reference genome GRCz11 using 10X Genomics Cellranger software 6.1.2. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Body,,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,tissue:Body|genotype:AB|age:6 dpf|treatment:LPS,GSM8703959,GSM8703959: LPS 10hr; Danio rerio; RNA Seq,GSM8703959 r1,GSM8703959,1,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP554457,,loader:fastq load.py,LPS_S11_L001_I1_001.fastq.gz LPS_S11_L001_R1_001.fastq.gz LPS_S11_L001_R2_001.fastq.gz,fastq fastq fastq,27204594943.0,214209409.0,GSM8703959 r1,0:8 1:28 2:91,A:5353386805;C:4418850048;G:5242873068;T:4476300884;N:1645414,8,28,91,,5353386805,4418850048,5242873068,4476300884,1645414,SRX27213774,SRS23662881,SRA2042619,"Jerison, Physics, University of Chicago","Jerison, Physics, University of Chicago",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-30,Larval,Larval,Trunk,Surface Structure
34505,SRR31854000,SRX27213774,SRS23662881,SRP554457,PRJNA1204318,Spatially structured inflammatory response in the presence of a uniform stimulus: RNAseq screen,GSE285534,Transcriptome Analysis,Inflammatory responses occur within the complex spatial context of tissues and organs  and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here  we used single cell RNA sequencing to screen for genes differentially expressed under LPS lipopolysaccharide and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis. Overall design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS P. Aeuruginosa  Sigma  or E3 alone vehicle control  for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification.,,,,LPS 10hr,GSM8703959,,source name:Body|tissue:Body|genotype:AB|age:6 dpf|treatment:LPS|geo loc name:missing|collection date:missing,LPS 10hr,Sequencing data was aligned to the zebrafish reference genome GRCz11 using 10X Genomics Cellranger software 6.1.2. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Body,,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,tissue:Body|genotype:AB|age:6 dpf|treatment:LPS,GSM8703959,GSM8703959: LPS 10hr; Danio rerio; RNA Seq,GSM8703959 r1,GSM8703959,1,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP554457,,loader:fastq load.py,LPS_S11_L002_I1_001.fastq.gz LPS_S11_L002_R1_001.fastq.gz LPS_S11_L002_R2_001.fastq.gz,fastq fastq fastq,27514945859.0,216653117.0,GSM8703959 r2,0:8 1:28 2:91,A:5407507765;C:4472892263;G:5312032344;T:4520956753;N:2044522,8,28,91,,5407507765,4472892263,5312032344,4520956753,2044522,SRX27213774,SRS23662881,SRA2042619,"Jerison, Physics, University of Chicago","Jerison, Physics, University of Chicago",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-30,Larval,Larval,Trunk,Surface Structure
34506,SRR31854001,SRX27213774,SRS23662881,SRP554457,PRJNA1204318,Spatially structured inflammatory response in the presence of a uniform stimulus: RNAseq screen,GSE285534,Transcriptome Analysis,Inflammatory responses occur within the complex spatial context of tissues and organs  and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here  we used single cell RNA sequencing to screen for genes differentially expressed under LPS lipopolysaccharide and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis. Overall design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS P. Aeuruginosa  Sigma  or E3 alone vehicle control  for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification.,,,,LPS 10hr,GSM8703959,,source name:Body|tissue:Body|genotype:AB|age:6 dpf|treatment:LPS|geo loc name:missing|collection date:missing,LPS 10hr,Sequencing data was aligned to the zebrafish reference genome GRCz11 using 10X Genomics Cellranger software 6.1.2. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Body,,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,tissue:Body|genotype:AB|age:6 dpf|treatment:LPS,GSM8703959,GSM8703959: LPS 10hr; Danio rerio; RNA Seq,GSM8703959 r1,GSM8703959,1,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP554457,,loader:fastq load.py,LPS_S11_L003_I1_001.fastq.gz LPS_S11_L003_R1_001.fastq.gz LPS_S11_L003_R2_001.fastq.gz,fastq fastq fastq,28512338962.0,224506606.0,GSM8703959 r3,0:8 1:28 2:91,A:5590192273;C:4644899622;G:5516199030;T:4676442556;N:2367665,8,28,91,,5590192273,4644899622,5516199030,4676442556,2367665,SRX27213774,SRS23662881,SRA2042619,"Jerison, Physics, University of Chicago","Jerison, Physics, University of Chicago",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-30,Larval,Larval,Trunk,Surface Structure
34507,SRR31854002,SRX27213774,SRS23662881,SRP554457,PRJNA1204318,Spatially structured inflammatory response in the presence of a uniform stimulus: RNAseq screen,GSE285534,Transcriptome Analysis,Inflammatory responses occur within the complex spatial context of tissues and organs  and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here  we used single cell RNA sequencing to screen for genes differentially expressed under LPS lipopolysaccharide and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis. Overall design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS P. Aeuruginosa  Sigma  or E3 alone vehicle control  for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification.,,,,LPS 10hr,GSM8703959,,source name:Body|tissue:Body|genotype:AB|age:6 dpf|treatment:LPS|geo loc name:missing|collection date:missing,LPS 10hr,Sequencing data was aligned to the zebrafish reference genome GRCz11 using 10X Genomics Cellranger software 6.1.2. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Body,,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,tissue:Body|genotype:AB|age:6 dpf|treatment:LPS,GSM8703959,GSM8703959: LPS 10hr; Danio rerio; RNA Seq,GSM8703959 r1,GSM8703959,1,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP554457,,loader:fastq load.py,LPS_S11_L004_I1_001.fastq.gz LPS_S11_L004_R1_001.fastq.gz LPS_S11_L004_R2_001.fastq.gz,fastq fastq fastq,27411098848.0,215835424.0,GSM8703959 r4,0:8 1:28 2:91,A:5383218071;C:4459553243;G:5297438054;T:4498601355;N:2212861,8,28,91,,5383218071,4459553243,5297438054,4498601355,2212861,SRX27213774,SRS23662881,SRA2042619,"Jerison, Physics, University of Chicago","Jerison, Physics, University of Chicago",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-30,Larval,Larval,Trunk,Surface Structure
36242,SRR33873799,SRX29085358,SRS25297146,SRP590547,PRJNA1272846,Organism wide contributions to systemic skeletal muscle repair in larval zebrafish.,GSE299146,Transcriptome Analysis,We developed a systemic muscle injury model in zebrafish. Single cell transcriptomic analysis of muscle and non muscle tissues revealed that systemic and local muscle injuries elicit distinct cellular molecular responses  both quantitatively and qualitatively. These studies suggest that large  and small scale muscle injuries activate different regenerative programs  resulting in either systemic or local repair. Overall design: To characterize the regenerative responses and signaling pathways activated post systemic or local muscle injury  we generated Tgactc1b:NTR mCherry transgenic zebrafish lines.At 4 dpf  transgenic larvae were treated with MTZ overnight to systemically injure all myofibers  or were subjected to local mechanical injury needlestick of 2 3 somites.Uninjured and systemically injured larvae were collected at 1  2  and 4 xxx post injury. Mechanically injured larvae were collected at 2 xxx post injury. Sequencing results were compared between uninjured  systemically injured  and mechanically injured siblings.,,,,larval trunk  2dpi Needle Stick,GSM9034433,,source name:Trunk|tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Needle Stick|batch:4/20/2022|geo loc name:missing|collection date:missing,larval trunk  2dpi Needle Stick,post sequencing  the Illumina output was processed using the CellRanger v8.0.1 pipeline to generate gene barcode count matrices. A custom reference genome was made with the “cellranger mkref” command  using the fasta file of zebrafish reference genome GRCz11 constructed from the Ensemble genome build https://useast.ensembl.org/Danio rerio/Info/Index and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Base call files for each sample from Illumina were demultiplexed into FASTQ reads. Then  the “cellranger count” pipeline was used to align sequencing reads in FASTQ files to the custom reference genome. Both exon and intron sequences were included during the alignment. The filtered gene barcode count matrices generated by “cellranger count” was used for downstream analysis. Datasets were integrated and analyzed using Seurat v4.4.0 package with R v4.4.2Stuart etal.  2019; Team  2024. Each sample count matrix was filtered for genes that were expressed in at least 3 cells and cells expressing at least 200 genes  followed by cell quality assessment usingcommonly used QC matrixes Ilicic et al.  2016. Cells having a unique number of genes between 200 and 6500  mitochondrial gene percentage <5 and total number of reads UMIs between 300and 35000 were used for downstream processing. Each dataset was independently normalizedand scaled using the “SCTransform” function  which is an improved method for normalization  that performs a variance stabilizing transformation using negative binomial regression Hafemeisterand Satija  2019. Standard integration workflow of Seurat was used to identify shared sources of variation across experiments as well as mutual nearest neighbors Butler et al.  2018; Haghverdiet al.  2018. Integration features were selected based on the top 6000 highly variable features using “SelectIntegrationFeatures” function nfeatures = 6000  which was used as input for the“anchor.features” argument of the “FindIntegrationAnchors” function. PCA analysis was performed on the 6000 variable features and the top 50 principal components selected based on the elbow plot heuristic  which measures the contribution of variation in each component. These 50 principal components were used in “FindNeighbors” and “FindClusters” functions to perform graph based clustering on a shared nearest neighbor graph Levine et al.  2015; Xu and Su 2015. Louvain algorithm was used for modularity optimization in cell clustering using “FindClusters” function. The resolution parameter res = 0.3 that determines the granularity of clusteringwas selected by visually inspecting clusters with resolutions ranging between 0.1 and 2.0 as well as clustree graph Zappia and Oshlack  2018. Uniform Manifold Approximation and Reduction UMAP was used for non linear dimensional reduction of the first 50 principal components and visualize the data using “RunUMAP” function Becht et al.  2018. Data was graphed using different plot functions  such as “DimPlot”  “VlnPlot”  “FeaturePlot”  “Dotplot” and “DoHeatmap”  to view the cell cluster identity and marker gene expression. Cell proportions were extracted using the “table” and “prop.table” functions. Differential gene expression for individual clusters was identified using Wilcoxon rank sum test in the “FindAllMarkers” function. Marker genes detected in at least 25% of the clustered cells and had a positive average log2FC were reported. Muscle cells identified from the complete dataset were subclustered using the “subset” function for subcluster analysis. The muscle subset was again normalized and scaled using the “SCTransform” function with glmGamPoi method Ahlmann Eltze and Huber  2021. Fifty principal components were used and the resolution parameter was set to 0.4. Downstream analysis was done as described above for the integrated analysis. We used a zebrafish single atlas Sur et al.  2023 to generate a database of markers for each tissue and cell type Table S1. The differentially expressed markers of each cluster were crossreferenced with our compiled database using our “DE Marker Scoring” algorithm Saraswathy et al.  2024. For every matching marker gene  one point was given to the respective cluster under the column name with matching cell identity. Iteration over every marker gene was performed to generate a scoring matrix with varying points for each cluster against the different cell identities compiled in the database Table S2  sheet: scoring. The “phyper” function in R was then used to calculate one tailed binomial probabilities using hypergeometric distribution for the total score obtained from each cluster against each cell identity in the database Table S2  sheet: Binomial probability. −log10 of probability values were obtained for plotting the heatmap Table S2  sheet:−log10P. The resulting values were scaled from 0 to 100 and plotted as a heatmap using GraphPad prism. Each cluster was given an identity based on the maximum −log10 p score obtained in the heatmap. The top DE markers of clusters with ambiguous scores were manually annotated using the “ident genes” from the zebrafish single atlas Sur et al.  2023 and literature search McKellar et al.  2021. Top DE markers generated for each cluster is given in Table S3  sheet:topDEmarkers.all.clusters “RenameIdents” function was used to assign identity to each cluster. To confirm the assigned cluster identities  enrichment of classical markers of respective cell types were tested using Dot plot. The R package CellChat v2.1.2 was used to evaluate regenerative cell cell interactions post local and systemic muscle injury Jin et al.  2021. CellChat models the probability of cell cell communication by integrating our gene expression data with a database of known interaction between signaling ligands  receptors  and their cofactors CellChatDB. The RNA data was used to create CellChat object using “createCellChat” function  followed by the recommended preprocessing functions with default parameters for the analysis of individual datasets. Truncated mean method with 10% trimmed observation was used to compute average gene expression per cell group for the complete dataset. The default trimean method was used to compute average gene expression for the CellChat analysis. CellChatDB.zebrafish was used to infer cell cell communication. All categories of ligand receptor interactions in the database were used in the analysis. Communications involving less than 10 cells were excluded. The “netAnalysis computeCentrality” function was used to calculate network centrality scores at each time point. Functions such as “netVisual circle”  “netAnalysis contribution”  “netVisual aggregate”  “netVisual bubble”  “netAnalysis signalingRole heatmap”  and “netAnalysis signalingRole scatter” were used to generate different plots used in this paper. Assembly: zebrafish reference genome GRCz11 and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Supplementary files format and content: Compressed Filtered Feature and Barcode files as .tsv file and count matrices in .mtx file format.,Trunk,Fish were treated with 12 hours of metronidazole or were stuck locally with a needle,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell 3’ Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,Larval zebrafish of 4 dpf underwent drug treatments or needle stick injuries for muscle ablation,tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Needle Stick|batch:4/20/2022,GSM9034433,GSM9034433: larval trunk  2dpi Needle Stick; Danio rerio; RNA Seq,GSM9034433 r1,GSM9034433,1,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell three prime Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP590547,,,AJAH-ACTC_NTR_Mcherry-Needlestick-2dpi-NS-2dpi-lib1_S1_L003_R1_001.fastq.gz AJAH-ACTC_NTR_Mcherry-Needlestick-2dpi-NS-2dpi-lib1_S1_L003_R2_001.fastq.gz,fastq fastq,73442728978.0,412599601.0,GSM9034433 r1,0:28 1:150,A:21212027449;C:16424751525;G:17879456991;T:17925559458;N:933555,28,150,,,21212027449,16424751525,17879456991,17925559458,933555,SRX29085358,SRS25297146,SRA2144659,"Johnson Lab, Developmental Biology, Washington University in St.Louis","Johnson Lab, Developmental Biology, Washington University in St.Louis",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-06-06,Larval,Larval,Trunk,Surface Structure
36243,SRR33873800,SRX29085357,SRS25297145,SRP590547,PRJNA1272846,Organism wide contributions to systemic skeletal muscle repair in larval zebrafish.,GSE299146,Transcriptome Analysis,We developed a systemic muscle injury model in zebrafish. Single cell transcriptomic analysis of muscle and non muscle tissues revealed that systemic and local muscle injuries elicit distinct cellular molecular responses  both quantitatively and qualitatively. These studies suggest that large  and small scale muscle injuries activate different regenerative programs  resulting in either systemic or local repair. Overall design: To characterize the regenerative responses and signaling pathways activated post systemic or local muscle injury  we generated Tgactc1b:NTR mCherry transgenic zebrafish lines.At 4 dpf  transgenic larvae were treated with MTZ overnight to systemically injure all myofibers  or were subjected to local mechanical injury needlestick of 2 3 somites.Uninjured and systemically injured larvae were collected at 1  2  and 4 xxx post injury. Mechanically injured larvae were collected at 2 xxx post injury. Sequencing results were compared between uninjured  systemically injured  and mechanically injured siblings.,,,,larval trunk  4dpi mcherry MTZ,GSM9034432,,source name:Trunk|tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water + MTZ|batch:10/28/2022|geo loc name:missing|collection date:missing,larval trunk  4dpi mcherry MTZ,post sequencing  the Illumina output was processed using the CellRanger v8.0.1 pipeline to generate gene barcode count matrices. A custom reference genome was made with the “cellranger mkref” command  using the fasta file of zebrafish reference genome GRCz11 constructed from the Ensemble genome build https://useast.ensembl.org/Danio rerio/Info/Index and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Base call files for each sample from Illumina were demultiplexed into FASTQ reads. Then  the “cellranger count” pipeline was used to align sequencing reads in FASTQ files to the custom reference genome. Both exon and intron sequences were included during the alignment. The filtered gene barcode count matrices generated by “cellranger count” was used for downstream analysis. Datasets were integrated and analyzed using Seurat v4.4.0 package with R v4.4.2Stuart etal.  2019; Team  2024. Each sample count matrix was filtered for genes that were expressed in at least 3 cells and cells expressing at least 200 genes  followed by cell quality assessment usingcommonly used QC matrixes Ilicic et al.  2016. Cells having a unique number of genes between 200 and 6500  mitochondrial gene percentage <5 and total number of reads UMIs between 300and 35000 were used for downstream processing. Each dataset was independently normalizedand scaled using the “SCTransform” function  which is an improved method for normalization  that performs a variance stabilizing transformation using negative binomial regression Hafemeisterand Satija  2019. Standard integration workflow of Seurat was used to identify shared sources of variation across experiments as well as mutual nearest neighbors Butler et al.  2018; Haghverdiet al.  2018. Integration features were selected based on the top 6000 highly variable features using “SelectIntegrationFeatures” function nfeatures = 6000  which was used as input for the“anchor.features” argument of the “FindIntegrationAnchors” function. PCA analysis was performed on the 6000 variable features and the top 50 principal components selected based on the elbow plot heuristic  which measures the contribution of variation in each component. These 50 principal components were used in “FindNeighbors” and “FindClusters” functions to perform graph based clustering on a shared nearest neighbor graph Levine et al.  2015; Xu and Su 2015. Louvain algorithm was used for modularity optimization in cell clustering using “FindClusters” function. The resolution parameter res = 0.3 that determines the granularity of clusteringwas selected by visually inspecting clusters with resolutions ranging between 0.1 and 2.0 as well as clustree graph Zappia and Oshlack  2018. Uniform Manifold Approximation and Reduction UMAP was used for non linear dimensional reduction of the first 50 principal components and visualize the data using “RunUMAP” function Becht et al.  2018. Data was graphed using different plot functions  such as “DimPlot”  “VlnPlot”  “FeaturePlot”  “Dotplot” and “DoHeatmap”  to view the cell cluster identity and marker gene expression. Cell proportions were extracted using the “table” and “prop.table” functions. Differential gene expression for individual clusters was identified using Wilcoxon rank sum test in the “FindAllMarkers” function. Marker genes detected in at least 25% of the clustered cells and had a positive average log2FC were reported. Muscle cells identified from the complete dataset were subclustered using the “subset” function for subcluster analysis. The muscle subset was again normalized and scaled using the “SCTransform” function with glmGamPoi method Ahlmann Eltze and Huber  2021. Fifty principal components were used and the resolution parameter was set to 0.4. Downstream analysis was done as described above for the integrated analysis. We used a zebrafish single atlas Sur et al.  2023 to generate a database of markers for each tissue and cell type Table S1. The differentially expressed markers of each cluster were crossreferenced with our compiled database using our “DE Marker Scoring” algorithm Saraswathy et al.  2024. For every matching marker gene  one point was given to the respective cluster under the column name with matching cell identity. Iteration over every marker gene was performed to generate a scoring matrix with varying points for each cluster against the different cell identities compiled in the database Table S2  sheet: scoring. The “phyper” function in R was then used to calculate one tailed binomial probabilities using hypergeometric distribution for the total score obtained from each cluster against each cell identity in the database Table S2  sheet: Binomial probability. −log10 of probability values were obtained for plotting the heatmap Table S2  sheet:−log10P. The resulting values were scaled from 0 to 100 and plotted as a heatmap using GraphPad prism. Each cluster was given an identity based on the maximum −log10 p score obtained in the heatmap. The top DE markers of clusters with ambiguous scores were manually annotated using the “ident genes” from the zebrafish single atlas Sur et al.  2023 and literature search McKellar et al.  2021. Top DE markers generated for each cluster is given in Table S3  sheet:topDEmarkers.all.clusters “RenameIdents” function was used to assign identity to each cluster. To confirm the assigned cluster identities  enrichment of classical markers of respective cell types were tested using Dot plot. The R package CellChat v2.1.2 was used to evaluate regenerative cell cell interactions post local and systemic muscle injury Jin et al.  2021. CellChat models the probability of cell cell communication by integrating our gene expression data with a database of known interaction between signaling ligands  receptors  and their cofactors CellChatDB. The RNA data was used to create CellChat object using “createCellChat” function  followed by the recommended preprocessing functions with default parameters for the analysis of individual datasets. Truncated mean method with 10% trimmed observation was used to compute average gene expression per cell group for the complete dataset. The default trimean method was used to compute average gene expression for the CellChat analysis. CellChatDB.zebrafish was used to infer cell cell communication. All categories of ligand receptor interactions in the database were used in the analysis. Communications involving less than 10 cells were excluded. The “netAnalysis computeCentrality” function was used to calculate network centrality scores at each time point. Functions such as “netVisual circle”  “netAnalysis contribution”  “netVisual aggregate”  “netVisual bubble”  “netAnalysis signalingRole heatmap”  and “netAnalysis signalingRole scatter” were used to generate different plots used in this paper. Assembly: zebrafish reference genome GRCz11 and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Supplementary files format and content: Compressed Filtered Feature and Barcode files as .tsv file and count matrices in .mtx file format.,Trunk,Fish were treated with 12 hours of metronidazole or were stuck locally with a needle,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell 3’ Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,Larval zebrafish of 4 dpf underwent drug treatments or needle stick injuries for muscle ablation,tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water + MTZ|batch:10/28/2022,GSM9034432,GSM9034432: larval trunk  4dpi mcherry MTZ; Danio rerio; RNA Seq,GSM9034432 r1,GSM9034432,1,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell three prime Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP590547,,,AJAH-18300_Red-18300_mCherry_Positive_4dpi-lib1_S2_L004_R1_001.fastq.gz AJAH-18300_Red-18300_mCherry_Positive_4dpi-lib1_S2_L004_R2_001.fastq.gz,fastq fastq,109491443482.0,615120469.0,GSM9034432 r1,0:28 1:150,A:31642210635;C:24956118743;G:26943821428;T:25945839682;N:3452994,28,150,,,31642210635,24956118743,26943821428,25945839682,3452994,SRX29085357,SRS25297145,SRA2144659,"Johnson Lab, Developmental Biology, Washington University in St.Louis","Johnson Lab, Developmental Biology, Washington University in St.Louis",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-06-06,Larval,Larval,Trunk,Surface Structure
36244,SRR33873801,SRX29085356,SRS25297144,SRP590547,PRJNA1272846,Organism wide contributions to systemic skeletal muscle repair in larval zebrafish.,GSE299146,Transcriptome Analysis,We developed a systemic muscle injury model in zebrafish. Single cell transcriptomic analysis of muscle and non muscle tissues revealed that systemic and local muscle injuries elicit distinct cellular molecular responses  both quantitatively and qualitatively. These studies suggest that large  and small scale muscle injuries activate different regenerative programs  resulting in either systemic or local repair. Overall design: To characterize the regenerative responses and signaling pathways activated post systemic or local muscle injury  we generated Tgactc1b:NTR mCherry transgenic zebrafish lines.At 4 dpf  transgenic larvae were treated with MTZ overnight to systemically injure all myofibers  or were subjected to local mechanical injury needlestick of 2 3 somites.Uninjured and systemically injured larvae were collected at 1  2  and 4 xxx post injury. Mechanically injured larvae were collected at 2 xxx post injury. Sequencing results were compared between uninjured  systemically injured  and mechanically injured siblings.,,,,larval trunk  4dpi Negative Control,GSM9034431,,source name:Trunk|tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water|batch:10/28/2022|geo loc name:missing|collection date:missing,larval trunk  4dpi Negative Control,post sequencing  the Illumina output was processed using the CellRanger v8.0.1 pipeline to generate gene barcode count matrices. A custom reference genome was made with the “cellranger mkref” command  using the fasta file of zebrafish reference genome GRCz11 constructed from the Ensemble genome build https://useast.ensembl.org/Danio rerio/Info/Index and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Base call files for each sample from Illumina were demultiplexed into FASTQ reads. Then  the “cellranger count” pipeline was used to align sequencing reads in FASTQ files to the custom reference genome. Both exon and intron sequences were included during the alignment. The filtered gene barcode count matrices generated by “cellranger count” was used for downstream analysis. Datasets were integrated and analyzed using Seurat v4.4.0 package with R v4.4.2Stuart etal.  2019; Team  2024. Each sample count matrix was filtered for genes that were expressed in at least 3 cells and cells expressing at least 200 genes  followed by cell quality assessment usingcommonly used QC matrixes Ilicic et al.  2016. Cells having a unique number of genes between 200 and 6500  mitochondrial gene percentage <5 and total number of reads UMIs between 300and 35000 were used for downstream processing. Each dataset was independently normalizedand scaled using the “SCTransform” function  which is an improved method for normalization  that performs a variance stabilizing transformation using negative binomial regression Hafemeisterand Satija  2019. Standard integration workflow of Seurat was used to identify shared sources of variation across experiments as well as mutual nearest neighbors Butler et al.  2018; Haghverdiet al.  2018. Integration features were selected based on the top 6000 highly variable features using “SelectIntegrationFeatures” function nfeatures = 6000  which was used as input for the“anchor.features” argument of the “FindIntegrationAnchors” function. PCA analysis was performed on the 6000 variable features and the top 50 principal components selected based on the elbow plot heuristic  which measures the contribution of variation in each component. These 50 principal components were used in “FindNeighbors” and “FindClusters” functions to perform graph based clustering on a shared nearest neighbor graph Levine et al.  2015; Xu and Su 2015. Louvain algorithm was used for modularity optimization in cell clustering using “FindClusters” function. The resolution parameter res = 0.3 that determines the granularity of clusteringwas selected by visually inspecting clusters with resolutions ranging between 0.1 and 2.0 as well as clustree graph Zappia and Oshlack  2018. Uniform Manifold Approximation and Reduction UMAP was used for non linear dimensional reduction of the first 50 principal components and visualize the data using “RunUMAP” function Becht et al.  2018. Data was graphed using different plot functions  such as “DimPlot”  “VlnPlot”  “FeaturePlot”  “Dotplot” and “DoHeatmap”  to view the cell cluster identity and marker gene expression. Cell proportions were extracted using the “table” and “prop.table” functions. Differential gene expression for individual clusters was identified using Wilcoxon rank sum test in the “FindAllMarkers” function. Marker genes detected in at least 25% of the clustered cells and had a positive average log2FC were reported. Muscle cells identified from the complete dataset were subclustered using the “subset” function for subcluster analysis. The muscle subset was again normalized and scaled using the “SCTransform” function with glmGamPoi method Ahlmann Eltze and Huber  2021. Fifty principal components were used and the resolution parameter was set to 0.4. Downstream analysis was done as described above for the integrated analysis. We used a zebrafish single atlas Sur et al.  2023 to generate a database of markers for each tissue and cell type Table S1. The differentially expressed markers of each cluster were crossreferenced with our compiled database using our “DE Marker Scoring” algorithm Saraswathy et al.  2024. For every matching marker gene  one point was given to the respective cluster under the column name with matching cell identity. Iteration over every marker gene was performed to generate a scoring matrix with varying points for each cluster against the different cell identities compiled in the database Table S2  sheet: scoring. The “phyper” function in R was then used to calculate one tailed binomial probabilities using hypergeometric distribution for the total score obtained from each cluster against each cell identity in the database Table S2  sheet: Binomial probability. −log10 of probability values were obtained for plotting the heatmap Table S2  sheet:−log10P. The resulting values were scaled from 0 to 100 and plotted as a heatmap using GraphPad prism. Each cluster was given an identity based on the maximum −log10 p score obtained in the heatmap. The top DE markers of clusters with ambiguous scores were manually annotated using the “ident genes” from the zebrafish single atlas Sur et al.  2023 and literature search McKellar et al.  2021. Top DE markers generated for each cluster is given in Table S3  sheet:topDEmarkers.all.clusters “RenameIdents” function was used to assign identity to each cluster. To confirm the assigned cluster identities  enrichment of classical markers of respective cell types were tested using Dot plot. The R package CellChat v2.1.2 was used to evaluate regenerative cell cell interactions post local and systemic muscle injury Jin et al.  2021. CellChat models the probability of cell cell communication by integrating our gene expression data with a database of known interaction between signaling ligands  receptors  and their cofactors CellChatDB. The RNA data was used to create CellChat object using “createCellChat” function  followed by the recommended preprocessing functions with default parameters for the analysis of individual datasets. Truncated mean method with 10% trimmed observation was used to compute average gene expression per cell group for the complete dataset. The default trimean method was used to compute average gene expression for the CellChat analysis. CellChatDB.zebrafish was used to infer cell cell communication. All categories of ligand receptor interactions in the database were used in the analysis. Communications involving less than 10 cells were excluded. The “netAnalysis computeCentrality” function was used to calculate network centrality scores at each time point. Functions such as “netVisual circle”  “netAnalysis contribution”  “netVisual aggregate”  “netVisual bubble”  “netAnalysis signalingRole heatmap”  and “netAnalysis signalingRole scatter” were used to generate different plots used in this paper. Assembly: zebrafish reference genome GRCz11 and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Supplementary files format and content: Compressed Filtered Feature and Barcode files as .tsv file and count matrices in .mtx file format.,Trunk,Fish were treated with 12 hours of metronidazole or were stuck locally with a needle,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell 3’ Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,Larval zebrafish of 4 dpf underwent drug treatments or needle stick injuries for muscle ablation,tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water|batch:10/28/2022,GSM9034431,GSM9034431: larval trunk  4dpi Negative Control; Danio rerio; RNA Seq,GSM9034431 r1,GSM9034431,1,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell three prime Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP590547,,,AJAH-18300_Green-18300_Negative_Control_4dpi-lib1_S1_L004_R1_001.fastq.gz AJAH-18300_Green-18300_Negative_Control_4dpi-lib1_S1_L004_R2_001.fastq.gz,fastq fastq,120050343140.0,674440130.0,GSM9034431 r1,0:28 1:150,A:34219257803;C:27603489363;G:29252474045;T:28971358956;N:3762973,28,150,,,34219257803,27603489363,29252474045,28971358956,3762973,SRX29085356,SRS25297144,SRA2144659,"Johnson Lab, Developmental Biology, Washington University in St.Louis","Johnson Lab, Developmental Biology, Washington University in St.Louis",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-06-06,Larval,Larval,Trunk,Surface Structure
36245,SRR33873802,SRX29085355,SRS25297143,SRP590547,PRJNA1272846,Organism wide contributions to systemic skeletal muscle repair in larval zebrafish.,GSE299146,Transcriptome Analysis,We developed a systemic muscle injury model in zebrafish. Single cell transcriptomic analysis of muscle and non muscle tissues revealed that systemic and local muscle injuries elicit distinct cellular molecular responses  both quantitatively and qualitatively. These studies suggest that large  and small scale muscle injuries activate different regenerative programs  resulting in either systemic or local repair. Overall design: To characterize the regenerative responses and signaling pathways activated post systemic or local muscle injury  we generated Tgactc1b:NTR mCherry transgenic zebrafish lines.At 4 dpf  transgenic larvae were treated with MTZ overnight to systemically injure all myofibers  or were subjected to local mechanical injury needlestick of 2 3 somites.Uninjured and systemically injured larvae were collected at 1  2  and 4 xxx post injury. Mechanically injured larvae were collected at 2 xxx post injury. Sequencing results were compared between uninjured  systemically injured  and mechanically injured siblings.,,,,larval trunk  2dpi mcherry MTZ,GSM9034430,,source name:Trunk|tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water + MTZ|batch:10/26/2022|geo loc name:missing|collection date:missing,larval trunk  2dpi mcherry MTZ,post sequencing  the Illumina output was processed using the CellRanger v8.0.1 pipeline to generate gene barcode count matrices. A custom reference genome was made with the “cellranger mkref” command  using the fasta file of zebrafish reference genome GRCz11 constructed from the Ensemble genome build https://useast.ensembl.org/Danio rerio/Info/Index and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Base call files for each sample from Illumina were demultiplexed into FASTQ reads. Then  the “cellranger count” pipeline was used to align sequencing reads in FASTQ files to the custom reference genome. Both exon and intron sequences were included during the alignment. The filtered gene barcode count matrices generated by “cellranger count” was used for downstream analysis. Datasets were integrated and analyzed using Seurat v4.4.0 package with R v4.4.2Stuart etal.  2019; Team  2024. Each sample count matrix was filtered for genes that were expressed in at least 3 cells and cells expressing at least 200 genes  followed by cell quality assessment usingcommonly used QC matrixes Ilicic et al.  2016. Cells having a unique number of genes between 200 and 6500  mitochondrial gene percentage <5 and total number of reads UMIs between 300and 35000 were used for downstream processing. Each dataset was independently normalizedand scaled using the “SCTransform” function  which is an improved method for normalization  that performs a variance stabilizing transformation using negative binomial regression Hafemeisterand Satija  2019. Standard integration workflow of Seurat was used to identify shared sources of variation across experiments as well as mutual nearest neighbors Butler et al.  2018; Haghverdiet al.  2018. Integration features were selected based on the top 6000 highly variable features using “SelectIntegrationFeatures” function nfeatures = 6000  which was used as input for the“anchor.features” argument of the “FindIntegrationAnchors” function. PCA analysis was performed on the 6000 variable features and the top 50 principal components selected based on the elbow plot heuristic  which measures the contribution of variation in each component. These 50 principal components were used in “FindNeighbors” and “FindClusters” functions to perform graph based clustering on a shared nearest neighbor graph Levine et al.  2015; Xu and Su 2015. Louvain algorithm was used for modularity optimization in cell clustering using “FindClusters” function. The resolution parameter res = 0.3 that determines the granularity of clusteringwas selected by visually inspecting clusters with resolutions ranging between 0.1 and 2.0 as well as clustree graph Zappia and Oshlack  2018. Uniform Manifold Approximation and Reduction UMAP was used for non linear dimensional reduction of the first 50 principal components and visualize the data using “RunUMAP” function Becht et al.  2018. Data was graphed using different plot functions  such as “DimPlot”  “VlnPlot”  “FeaturePlot”  “Dotplot” and “DoHeatmap”  to view the cell cluster identity and marker gene expression. Cell proportions were extracted using the “table” and “prop.table” functions. Differential gene expression for individual clusters was identified using Wilcoxon rank sum test in the “FindAllMarkers” function. Marker genes detected in at least 25% of the clustered cells and had a positive average log2FC were reported. Muscle cells identified from the complete dataset were subclustered using the “subset” function for subcluster analysis. The muscle subset was again normalized and scaled using the “SCTransform” function with glmGamPoi method Ahlmann Eltze and Huber  2021. Fifty principal components were used and the resolution parameter was set to 0.4. Downstream analysis was done as described above for the integrated analysis. We used a zebrafish single atlas Sur et al.  2023 to generate a database of markers for each tissue and cell type Table S1. The differentially expressed markers of each cluster were crossreferenced with our compiled database using our “DE Marker Scoring” algorithm Saraswathy et al.  2024. For every matching marker gene  one point was given to the respective cluster under the column name with matching cell identity. Iteration over every marker gene was performed to generate a scoring matrix with varying points for each cluster against the different cell identities compiled in the database Table S2  sheet: scoring. The “phyper” function in R was then used to calculate one tailed binomial probabilities using hypergeometric distribution for the total score obtained from each cluster against each cell identity in the database Table S2  sheet: Binomial probability. −log10 of probability values were obtained for plotting the heatmap Table S2  sheet:−log10P. The resulting values were scaled from 0 to 100 and plotted as a heatmap using GraphPad prism. Each cluster was given an identity based on the maximum −log10 p score obtained in the heatmap. The top DE markers of clusters with ambiguous scores were manually annotated using the “ident genes” from the zebrafish single atlas Sur et al.  2023 and literature search McKellar et al.  2021. Top DE markers generated for each cluster is given in Table S3  sheet:topDEmarkers.all.clusters “RenameIdents” function was used to assign identity to each cluster. To confirm the assigned cluster identities  enrichment of classical markers of respective cell types were tested using Dot plot. The R package CellChat v2.1.2 was used to evaluate regenerative cell cell interactions post local and systemic muscle injury Jin et al.  2021. CellChat models the probability of cell cell communication by integrating our gene expression data with a database of known interaction between signaling ligands  receptors  and their cofactors CellChatDB. The RNA data was used to create CellChat object using “createCellChat” function  followed by the recommended preprocessing functions with default parameters for the analysis of individual datasets. Truncated mean method with 10% trimmed observation was used to compute average gene expression per cell group for the complete dataset. The default trimean method was used to compute average gene expression for the CellChat analysis. CellChatDB.zebrafish was used to infer cell cell communication. All categories of ligand receptor interactions in the database were used in the analysis. Communications involving less than 10 cells were excluded. The “netAnalysis computeCentrality” function was used to calculate network centrality scores at each time point. Functions such as “netVisual circle”  “netAnalysis contribution”  “netVisual aggregate”  “netVisual bubble”  “netAnalysis signalingRole heatmap”  and “netAnalysis signalingRole scatter” were used to generate different plots used in this paper. Assembly: zebrafish reference genome GRCz11 and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Supplementary files format and content: Compressed Filtered Feature and Barcode files as .tsv file and count matrices in .mtx file format.,Trunk,Fish were treated with 12 hours of metronidazole or were stuck locally with a needle,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell 3’ Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,Larval zebrafish of 4 dpf underwent drug treatments or needle stick injuries for muscle ablation,tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water + MTZ|batch:10/26/2022,GSM9034430,GSM9034430: larval trunk  2dpi mcherry MTZ; Danio rerio; RNA Seq,GSM9034430 r1,GSM9034430,1,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell three prime Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP590547,,,AJAH-18300_Red-18300_mCherry_Positive_2dpi-lib1_S2_L004_R1_001.fastq.gz AJAH-18300_Red-18300_mCherry_Positive_2dpi-lib1_S2_L004_R2_001.fastq.gz,fastq fastq,86534465752.0,486148684.0,GSM9034430 r1,0:28 1:150,A:23591959992;C:20534495856;G:22206815673;T:20199626171;N:1568060,28,150,,,23591959992,20534495856,22206815673,20199626171,1568060,SRX29085355,SRS25297143,SRA2144659,"Johnson Lab, Developmental Biology, Washington University in St.Louis","Johnson Lab, Developmental Biology, Washington University in St.Louis",2,0.01419,0.94664,0.00513,0.17395,0.99504,0.8396,0.29625,0.66798,28,150,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-06-06,Larval,Larval,Trunk,Surface Structure
36246,SRR33873803,SRX29085354,SRS25297142,SRP590547,PRJNA1272846,Organism wide contributions to systemic skeletal muscle repair in larval zebrafish.,GSE299146,Transcriptome Analysis,We developed a systemic muscle injury model in zebrafish. Single cell transcriptomic analysis of muscle and non muscle tissues revealed that systemic and local muscle injuries elicit distinct cellular molecular responses  both quantitatively and qualitatively. These studies suggest that large  and small scale muscle injuries activate different regenerative programs  resulting in either systemic or local repair. Overall design: To characterize the regenerative responses and signaling pathways activated post systemic or local muscle injury  we generated Tgactc1b:NTR mCherry transgenic zebrafish lines.At 4 dpf  transgenic larvae were treated with MTZ overnight to systemically injure all myofibers  or were subjected to local mechanical injury needlestick of 2 3 somites.Uninjured and systemically injured larvae were collected at 1  2  and 4 xxx post injury. Mechanically injured larvae were collected at 2 xxx post injury. Sequencing results were compared between uninjured  systemically injured  and mechanically injured siblings.,,,,larval trunk  2dpi Negative Control,GSM9034429,,source name:Trunk|tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water|batch:10/26/2022|geo loc name:missing|collection date:missing,larval trunk  2dpi Negative Control,post sequencing  the Illumina output was processed using the CellRanger v8.0.1 pipeline to generate gene barcode count matrices. A custom reference genome was made with the “cellranger mkref” command  using the fasta file of zebrafish reference genome GRCz11 constructed from the Ensemble genome build https://useast.ensembl.org/Danio rerio/Info/Index and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Base call files for each sample from Illumina were demultiplexed into FASTQ reads. Then  the “cellranger count” pipeline was used to align sequencing reads in FASTQ files to the custom reference genome. Both exon and intron sequences were included during the alignment. The filtered gene barcode count matrices generated by “cellranger count” was used for downstream analysis. Datasets were integrated and analyzed using Seurat v4.4.0 package with R v4.4.2Stuart etal.  2019; Team  2024. Each sample count matrix was filtered for genes that were expressed in at least 3 cells and cells expressing at least 200 genes  followed by cell quality assessment usingcommonly used QC matrixes Ilicic et al.  2016. Cells having a unique number of genes between 200 and 6500  mitochondrial gene percentage <5 and total number of reads UMIs between 300and 35000 were used for downstream processing. Each dataset was independently normalizedand scaled using the “SCTransform” function  which is an improved method for normalization  that performs a variance stabilizing transformation using negative binomial regression Hafemeisterand Satija  2019. Standard integration workflow of Seurat was used to identify shared sources of variation across experiments as well as mutual nearest neighbors Butler et al.  2018; Haghverdiet al.  2018. Integration features were selected based on the top 6000 highly variable features using “SelectIntegrationFeatures” function nfeatures = 6000  which was used as input for the“anchor.features” argument of the “FindIntegrationAnchors” function. PCA analysis was performed on the 6000 variable features and the top 50 principal components selected based on the elbow plot heuristic  which measures the contribution of variation in each component. These 50 principal components were used in “FindNeighbors” and “FindClusters” functions to perform graph based clustering on a shared nearest neighbor graph Levine et al.  2015; Xu and Su 2015. Louvain algorithm was used for modularity optimization in cell clustering using “FindClusters” function. The resolution parameter res = 0.3 that determines the granularity of clusteringwas selected by visually inspecting clusters with resolutions ranging between 0.1 and 2.0 as well as clustree graph Zappia and Oshlack  2018. Uniform Manifold Approximation and Reduction UMAP was used for non linear dimensional reduction of the first 50 principal components and visualize the data using “RunUMAP” function Becht et al.  2018. Data was graphed using different plot functions  such as “DimPlot”  “VlnPlot”  “FeaturePlot”  “Dotplot” and “DoHeatmap”  to view the cell cluster identity and marker gene expression. Cell proportions were extracted using the “table” and “prop.table” functions. Differential gene expression for individual clusters was identified using Wilcoxon rank sum test in the “FindAllMarkers” function. Marker genes detected in at least 25% of the clustered cells and had a positive average log2FC were reported. Muscle cells identified from the complete dataset were subclustered using the “subset” function for subcluster analysis. The muscle subset was again normalized and scaled using the “SCTransform” function with glmGamPoi method Ahlmann Eltze and Huber  2021. Fifty principal components were used and the resolution parameter was set to 0.4. Downstream analysis was done as described above for the integrated analysis. We used a zebrafish single atlas Sur et al.  2023 to generate a database of markers for each tissue and cell type Table S1. The differentially expressed markers of each cluster were crossreferenced with our compiled database using our “DE Marker Scoring” algorithm Saraswathy et al.  2024. For every matching marker gene  one point was given to the respective cluster under the column name with matching cell identity. Iteration over every marker gene was performed to generate a scoring matrix with varying points for each cluster against the different cell identities compiled in the database Table S2  sheet: scoring. The “phyper” function in R was then used to calculate one tailed binomial probabilities using hypergeometric distribution for the total score obtained from each cluster against each cell identity in the database Table S2  sheet: Binomial probability. −log10 of probability values were obtained for plotting the heatmap Table S2  sheet:−log10P. The resulting values were scaled from 0 to 100 and plotted as a heatmap using GraphPad prism. Each cluster was given an identity based on the maximum −log10 p score obtained in the heatmap. The top DE markers of clusters with ambiguous scores were manually annotated using the “ident genes” from the zebrafish single atlas Sur et al.  2023 and literature search McKellar et al.  2021. Top DE markers generated for each cluster is given in Table S3  sheet:topDEmarkers.all.clusters “RenameIdents” function was used to assign identity to each cluster. To confirm the assigned cluster identities  enrichment of classical markers of respective cell types were tested using Dot plot. The R package CellChat v2.1.2 was used to evaluate regenerative cell cell interactions post local and systemic muscle injury Jin et al.  2021. CellChat models the probability of cell cell communication by integrating our gene expression data with a database of known interaction between signaling ligands  receptors  and their cofactors CellChatDB. The RNA data was used to create CellChat object using “createCellChat” function  followed by the recommended preprocessing functions with default parameters for the analysis of individual datasets. Truncated mean method with 10% trimmed observation was used to compute average gene expression per cell group for the complete dataset. The default trimean method was used to compute average gene expression for the CellChat analysis. CellChatDB.zebrafish was used to infer cell cell communication. All categories of ligand receptor interactions in the database were used in the analysis. Communications involving less than 10 cells were excluded. The “netAnalysis computeCentrality” function was used to calculate network centrality scores at each time point. Functions such as “netVisual circle”  “netAnalysis contribution”  “netVisual aggregate”  “netVisual bubble”  “netAnalysis signalingRole heatmap”  and “netAnalysis signalingRole scatter” were used to generate different plots used in this paper. Assembly: zebrafish reference genome GRCz11 and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Supplementary files format and content: Compressed Filtered Feature and Barcode files as .tsv file and count matrices in .mtx file format.,Trunk,Fish were treated with 12 hours of metronidazole or were stuck locally with a needle,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell 3’ Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,Larval zebrafish of 4 dpf underwent drug treatments or needle stick injuries for muscle ablation,tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water|batch:10/26/2022,GSM9034429,GSM9034429: larval trunk  2dpi Negative Control; Danio rerio; RNA Seq,GSM9034429 r1,GSM9034429,1,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell three prime Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP590547,,,AJAH-18300_Green-18300_Negative_Control-lib1_S1_L004_R1_001.fastq.gz AJAH-18300_Green-18300_Negative_Control-lib1_S1_L004_R2_001.fastq.gz,fastq fastq,81637706044.0,458638798.0,GSM9034429 r1,0:28 1:150,A:23244690048;C:18579650528;G:19634226269;T:20177635070;N:1504129,28,150,,,23244690048,18579650528,19634226269,20177635070,1504129,SRX29085354,SRS25297142,SRA2144659,"Johnson Lab, Developmental Biology, Washington University in St.Louis","Johnson Lab, Developmental Biology, Washington University in St.Louis",2,0.0091,0.93772,0.00313,0.1383,0.99446,0.82698,0.33858,0.5389,28,150,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-06-06,Larval,Larval,Trunk,Surface Structure
36247,SRR33873804,SRX29085353,SRS25297141,SRP590547,PRJNA1272846,Organism wide contributions to systemic skeletal muscle repair in larval zebrafish.,GSE299146,Transcriptome Analysis,We developed a systemic muscle injury model in zebrafish. Single cell transcriptomic analysis of muscle and non muscle tissues revealed that systemic and local muscle injuries elicit distinct cellular molecular responses  both quantitatively and qualitatively. These studies suggest that large  and small scale muscle injuries activate different regenerative programs  resulting in either systemic or local repair. Overall design: To characterize the regenerative responses and signaling pathways activated post systemic or local muscle injury  we generated Tgactc1b:NTR mCherry transgenic zebrafish lines.At 4 dpf  transgenic larvae were treated with MTZ overnight to systemically injure all myofibers  or were subjected to local mechanical injury needlestick of 2 3 somites.Uninjured and systemically injured larvae were collected at 1  2  and 4 xxx post injury. Mechanically injured larvae were collected at 2 xxx post injury. Sequencing results were compared between uninjured  systemically injured  and mechanically injured siblings.,,,,larval trunk  1dpi mcherry MTZ,GSM9034428,,source name:Trunk|tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water + MTZ|batch:10/25/2022|geo loc name:missing|collection date:missing,larval trunk  1dpi mcherry MTZ,post sequencing  the Illumina output was processed using the CellRanger v8.0.1 pipeline to generate gene barcode count matrices. A custom reference genome was made with the “cellranger mkref” command  using the fasta file of zebrafish reference genome GRCz11 constructed from the Ensemble genome build https://useast.ensembl.org/Danio rerio/Info/Index and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Base call files for each sample from Illumina were demultiplexed into FASTQ reads. Then  the “cellranger count” pipeline was used to align sequencing reads in FASTQ files to the custom reference genome. Both exon and intron sequences were included during the alignment. The filtered gene barcode count matrices generated by “cellranger count” was used for downstream analysis. Datasets were integrated and analyzed using Seurat v4.4.0 package with R v4.4.2Stuart etal.  2019; Team  2024. Each sample count matrix was filtered for genes that were expressed in at least 3 cells and cells expressing at least 200 genes  followed by cell quality assessment usingcommonly used QC matrixes Ilicic et al.  2016. Cells having a unique number of genes between 200 and 6500  mitochondrial gene percentage <5 and total number of reads UMIs between 300and 35000 were used for downstream processing. Each dataset was independently normalizedand scaled using the “SCTransform” function  which is an improved method for normalization  that performs a variance stabilizing transformation using negative binomial regression Hafemeisterand Satija  2019. Standard integration workflow of Seurat was used to identify shared sources of variation across experiments as well as mutual nearest neighbors Butler et al.  2018; Haghverdiet al.  2018. Integration features were selected based on the top 6000 highly variable features using “SelectIntegrationFeatures” function nfeatures = 6000  which was used as input for the“anchor.features” argument of the “FindIntegrationAnchors” function. PCA analysis was performed on the 6000 variable features and the top 50 principal components selected based on the elbow plot heuristic  which measures the contribution of variation in each component. These 50 principal components were used in “FindNeighbors” and “FindClusters” functions to perform graph based clustering on a shared nearest neighbor graph Levine et al.  2015; Xu and Su 2015. Louvain algorithm was used for modularity optimization in cell clustering using “FindClusters” function. The resolution parameter res = 0.3 that determines the granularity of clusteringwas selected by visually inspecting clusters with resolutions ranging between 0.1 and 2.0 as well as clustree graph Zappia and Oshlack  2018. Uniform Manifold Approximation and Reduction UMAP was used for non linear dimensional reduction of the first 50 principal components and visualize the data using “RunUMAP” function Becht et al.  2018. Data was graphed using different plot functions  such as “DimPlot”  “VlnPlot”  “FeaturePlot”  “Dotplot” and “DoHeatmap”  to view the cell cluster identity and marker gene expression. Cell proportions were extracted using the “table” and “prop.table” functions. Differential gene expression for individual clusters was identified using Wilcoxon rank sum test in the “FindAllMarkers” function. Marker genes detected in at least 25% of the clustered cells and had a positive average log2FC were reported. Muscle cells identified from the complete dataset were subclustered using the “subset” function for subcluster analysis. The muscle subset was again normalized and scaled using the “SCTransform” function with glmGamPoi method Ahlmann Eltze and Huber  2021. Fifty principal components were used and the resolution parameter was set to 0.4. Downstream analysis was done as described above for the integrated analysis. We used a zebrafish single atlas Sur et al.  2023 to generate a database of markers for each tissue and cell type Table S1. The differentially expressed markers of each cluster were crossreferenced with our compiled database using our “DE Marker Scoring” algorithm Saraswathy et al.  2024. For every matching marker gene  one point was given to the respective cluster under the column name with matching cell identity. Iteration over every marker gene was performed to generate a scoring matrix with varying points for each cluster against the different cell identities compiled in the database Table S2  sheet: scoring. The “phyper” function in R was then used to calculate one tailed binomial probabilities using hypergeometric distribution for the total score obtained from each cluster against each cell identity in the database Table S2  sheet: Binomial probability. −log10 of probability values were obtained for plotting the heatmap Table S2  sheet:−log10P. The resulting values were scaled from 0 to 100 and plotted as a heatmap using GraphPad prism. Each cluster was given an identity based on the maximum −log10 p score obtained in the heatmap. The top DE markers of clusters with ambiguous scores were manually annotated using the “ident genes” from the zebrafish single atlas Sur et al.  2023 and literature search McKellar et al.  2021. Top DE markers generated for each cluster is given in Table S3  sheet:topDEmarkers.all.clusters “RenameIdents” function was used to assign identity to each cluster. To confirm the assigned cluster identities  enrichment of classical markers of respective cell types were tested using Dot plot. The R package CellChat v2.1.2 was used to evaluate regenerative cell cell interactions post local and systemic muscle injury Jin et al.  2021. CellChat models the probability of cell cell communication by integrating our gene expression data with a database of known interaction between signaling ligands  receptors  and their cofactors CellChatDB. The RNA data was used to create CellChat object using “createCellChat” function  followed by the recommended preprocessing functions with default parameters for the analysis of individual datasets. Truncated mean method with 10% trimmed observation was used to compute average gene expression per cell group for the complete dataset. The default trimean method was used to compute average gene expression for the CellChat analysis. CellChatDB.zebrafish was used to infer cell cell communication. All categories of ligand receptor interactions in the database were used in the analysis. Communications involving less than 10 cells were excluded. The “netAnalysis computeCentrality” function was used to calculate network centrality scores at each time point. Functions such as “netVisual circle”  “netAnalysis contribution”  “netVisual aggregate”  “netVisual bubble”  “netAnalysis signalingRole heatmap”  and “netAnalysis signalingRole scatter” were used to generate different plots used in this paper. Assembly: zebrafish reference genome GRCz11 and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Supplementary files format and content: Compressed Filtered Feature and Barcode files as .tsv file and count matrices in .mtx file format.,Trunk,Fish were treated with 12 hours of metronidazole or were stuck locally with a needle,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell 3’ Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,Larval zebrafish of 4 dpf underwent drug treatments or needle stick injuries for muscle ablation,tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water + MTZ|batch:10/25/2022,GSM9034428,GSM9034428: larval trunk  1dpi mcherry MTZ; Danio rerio; RNA Seq,GSM9034428 r1,GSM9034428,1,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell three prime Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP590547,,,AJAH-18300_Red-18300_mCherry_Positive-lib1_S2_L004_R1_001.fastq.gz AJAH-18300_Red-18300_mCherry_Positive-lib1_S2_L004_R2_001.fastq.gz,fastq fastq,84014647022.0,471992399.0,GSM9034428 r1,0:28 1:150,A:24181834463;C:18988262388;G:20195117959;T:20647899177;N:1533035,28,150,,,24181834463,18988262388,20195117959,20647899177,1533035,SRX29085353,SRS25297141,SRA2144659,"Johnson Lab, Developmental Biology, Washington University in St.Louis","Johnson Lab, Developmental Biology, Washington University in St.Louis",2,0.00859,0.93077,0.00306,0.13947,0.99393,0.81807,0.39035,0.66419,28,150,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-06-06,Larval,Larval,Trunk,Surface Structure
36248,SRR33873805,SRX29085352,SRS25297140,SRP590547,PRJNA1272846,Organism wide contributions to systemic skeletal muscle repair in larval zebrafish.,GSE299146,Transcriptome Analysis,We developed a systemic muscle injury model in zebrafish. Single cell transcriptomic analysis of muscle and non muscle tissues revealed that systemic and local muscle injuries elicit distinct cellular molecular responses  both quantitatively and qualitatively. These studies suggest that large  and small scale muscle injuries activate different regenerative programs  resulting in either systemic or local repair. Overall design: To characterize the regenerative responses and signaling pathways activated post systemic or local muscle injury  we generated Tgactc1b:NTR mCherry transgenic zebrafish lines.At 4 dpf  transgenic larvae were treated with MTZ overnight to systemically injure all myofibers  or were subjected to local mechanical injury needlestick of 2 3 somites.Uninjured and systemically injured larvae were collected at 1  2  and 4 xxx post injury. Mechanically injured larvae were collected at 2 xxx post injury. Sequencing results were compared between uninjured  systemically injured  and mechanically injured siblings.,,,,larval trunk  1dpi Negative Control,GSM9034427,,source name:Trunk|tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water|batch:11/4/2024|geo loc name:missing|collection date:missing,larval trunk  1dpi Negative Control,post sequencing  the Illumina output was processed using the CellRanger v8.0.1 pipeline to generate gene barcode count matrices. A custom reference genome was made with the “cellranger mkref” command  using the fasta file of zebrafish reference genome GRCz11 constructed from the Ensemble genome build https://useast.ensembl.org/Danio rerio/Info/Index and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Base call files for each sample from Illumina were demultiplexed into FASTQ reads. Then  the “cellranger count” pipeline was used to align sequencing reads in FASTQ files to the custom reference genome. Both exon and intron sequences were included during the alignment. The filtered gene barcode count matrices generated by “cellranger count” was used for downstream analysis. Datasets were integrated and analyzed using Seurat v4.4.0 package with R v4.4.2Stuart etal.  2019; Team  2024. Each sample count matrix was filtered for genes that were expressed in at least 3 cells and cells expressing at least 200 genes  followed by cell quality assessment usingcommonly used QC matrixes Ilicic et al.  2016. Cells having a unique number of genes between 200 and 6500  mitochondrial gene percentage <5 and total number of reads UMIs between 300and 35000 were used for downstream processing. Each dataset was independently normalizedand scaled using the “SCTransform” function  which is an improved method for normalization  that performs a variance stabilizing transformation using negative binomial regression Hafemeisterand Satija  2019. Standard integration workflow of Seurat was used to identify shared sources of variation across experiments as well as mutual nearest neighbors Butler et al.  2018; Haghverdiet al.  2018. Integration features were selected based on the top 6000 highly variable features using “SelectIntegrationFeatures” function nfeatures = 6000  which was used as input for the“anchor.features” argument of the “FindIntegrationAnchors” function. PCA analysis was performed on the 6000 variable features and the top 50 principal components selected based on the elbow plot heuristic  which measures the contribution of variation in each component. These 50 principal components were used in “FindNeighbors” and “FindClusters” functions to perform graph based clustering on a shared nearest neighbor graph Levine et al.  2015; Xu and Su 2015. Louvain algorithm was used for modularity optimization in cell clustering using “FindClusters” function. The resolution parameter res = 0.3 that determines the granularity of clusteringwas selected by visually inspecting clusters with resolutions ranging between 0.1 and 2.0 as well as clustree graph Zappia and Oshlack  2018. Uniform Manifold Approximation and Reduction UMAP was used for non linear dimensional reduction of the first 50 principal components and visualize the data using “RunUMAP” function Becht et al.  2018. Data was graphed using different plot functions  such as “DimPlot”  “VlnPlot”  “FeaturePlot”  “Dotplot” and “DoHeatmap”  to view the cell cluster identity and marker gene expression. Cell proportions were extracted using the “table” and “prop.table” functions. Differential gene expression for individual clusters was identified using Wilcoxon rank sum test in the “FindAllMarkers” function. Marker genes detected in at least 25% of the clustered cells and had a positive average log2FC were reported. Muscle cells identified from the complete dataset were subclustered using the “subset” function for subcluster analysis. The muscle subset was again normalized and scaled using the “SCTransform” function with glmGamPoi method Ahlmann Eltze and Huber  2021. Fifty principal components were used and the resolution parameter was set to 0.4. Downstream analysis was done as described above for the integrated analysis. We used a zebrafish single atlas Sur et al.  2023 to generate a database of markers for each tissue and cell type Table S1. The differentially expressed markers of each cluster were crossreferenced with our compiled database using our “DE Marker Scoring” algorithm Saraswathy et al.  2024. For every matching marker gene  one point was given to the respective cluster under the column name with matching cell identity. Iteration over every marker gene was performed to generate a scoring matrix with varying points for each cluster against the different cell identities compiled in the database Table S2  sheet: scoring. The “phyper” function in R was then used to calculate one tailed binomial probabilities using hypergeometric distribution for the total score obtained from each cluster against each cell identity in the database Table S2  sheet: Binomial probability. −log10 of probability values were obtained for plotting the heatmap Table S2  sheet:−log10P. The resulting values were scaled from 0 to 100 and plotted as a heatmap using GraphPad prism. Each cluster was given an identity based on the maximum −log10 p score obtained in the heatmap. The top DE markers of clusters with ambiguous scores were manually annotated using the “ident genes” from the zebrafish single atlas Sur et al.  2023 and literature search McKellar et al.  2021. Top DE markers generated for each cluster is given in Table S3  sheet:topDEmarkers.all.clusters “RenameIdents” function was used to assign identity to each cluster. To confirm the assigned cluster identities  enrichment of classical markers of respective cell types were tested using Dot plot. The R package CellChat v2.1.2 was used to evaluate regenerative cell cell interactions post local and systemic muscle injury Jin et al.  2021. CellChat models the probability of cell cell communication by integrating our gene expression data with a database of known interaction between signaling ligands  receptors  and their cofactors CellChatDB. The RNA data was used to create CellChat object using “createCellChat” function  followed by the recommended preprocessing functions with default parameters for the analysis of individual datasets. Truncated mean method with 10% trimmed observation was used to compute average gene expression per cell group for the complete dataset. The default trimean method was used to compute average gene expression for the CellChat analysis. CellChatDB.zebrafish was used to infer cell cell communication. All categories of ligand receptor interactions in the database were used in the analysis. Communications involving less than 10 cells were excluded. The “netAnalysis computeCentrality” function was used to calculate network centrality scores at each time point. Functions such as “netVisual circle”  “netAnalysis contribution”  “netVisual aggregate”  “netVisual bubble”  “netAnalysis signalingRole heatmap”  and “netAnalysis signalingRole scatter” were used to generate different plots used in this paper. Assembly: zebrafish reference genome GRCz11 and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Supplementary files format and content: Compressed Filtered Feature and Barcode files as .tsv file and count matrices in .mtx file format.,Trunk,Fish were treated with 12 hours of metronidazole or were stuck locally with a needle,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell 3’ Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,Larval zebrafish of 4 dpf underwent drug treatments or needle stick injuries for muscle ablation,tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water|batch:11/4/2024,GSM9034427,GSM9034427: larval trunk  1dpi Negative Control; Danio rerio; RNA Seq,GSM9034427 r1,GSM9034427,1,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell three prime Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP590547,,,LIB065814-DIL01_22CNHTLT4_S90_L008_R1_001.fastq.gz LIB065814-DIL01_22CNHTLT4_S90_L008_R2_001.fastq.gz,fastq fastq,96199623993.0,537428067.0,GSM9034427 r1,0:28 1:151,A:26836117761;C:21626512077;G:22419696915;T:25306734573;N:10562667,28,151,,,26836117761,21626512077,22419696915,25306734573,10562667,SRX29085352,SRS25297140,SRA2144659,"Johnson Lab, Developmental Biology, Washington University in St.Louis","Johnson Lab, Developmental Biology, Washington University in St.Louis",2,0.01026,0.90959,0.00375,0.1621,0.99019,0.80945,0.41304,0.54052,28,151,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-06-06,Larval,Larval,Trunk,Surface Structure
43985,SRR6811830,SRX3768870,SRS3023387,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva F1 2 mRNA,GSM3032173,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva F1 2 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM3032173,GSM3032173: Larva F1 2 mRNA; Danio rerio; RNA Seq,GSM3032173,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032173,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,F1_2_wt_R1.fastq.gz F1_2_wt_R2.fastq.gz,fastq fastq,29997480708.0,241915167.0,GSM3032173 r1,0:26 1:98,A:8264355452;C:6830431714;G:7093261338;T:7804053400;N:5378804,26,98,,,8264355452,6830431714,7093261338,7804053400,5378804,SRX3768870,SRS3023387,SRA623333,GEO,Max Delbrück Center,2,0.00307,0.94486,0.00051,0.08199,0.99431,0.82509,0.36875,0.43599,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Larval,Larval,Trunk,Surface Structure
43986,SRR6811829,SRX3768869,SRS3023385,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva F1 1 mRNA,GSM3032172,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva F1 1 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM3032172,GSM3032172: Larva F1 1 mRNA; Danio rerio; RNA Seq,GSM3032172,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032172,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,F1_1_wt_R1.fastq.gz F1_1_wt_R2.fastq.gz,fastq fastq,26685876072.0,215208678.0,GSM3032172 r1,0:26 1:98,A:7365353958;C:6068313931;G:6251004125;T:6996410946;N:4793112,26,98,,,7365353958,6068313931,6251004125,6996410946,4793112,SRX3768869,SRS3023385,SRA623333,GEO,Max Delbrück Center,2,0.00255,0.93758,0.00046,0.08179,0.99515,0.82637,0.35368,0.46605,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Larval,Larval,Trunk,Surface Structure
43997,SRR6811818,SRX3768858,SRS3023376,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva 5 mRNA,GSM3032161,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva 5 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM3032161,GSM3032161: Larva 5 mRNA; Danio rerio; RNA Seq,GSM3032161,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032161,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,Z5_wt_R1.fastq.gz Z5_wt_R2.fastq.gz,fastq fastq,27409556812.0,221044813.0,GSM3032161 r1,0:26 1:98,A:7637677199;C:6210942203;G:6438364980;T:7117667800;N:4904630,26,98,,,7637677199,6210942203,6438364980,7117667800,4904630,SRX3768858,SRS3023376,SRA623333,GEO,Max Delbrück Center,2,0.00523,0.92734,0.0008,0.0687,0.98916,0.81479,0.44117,0.50243,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Larval,Larval,Trunk,Surface Structure
43998,SRR6811817,SRX3768857,SRS3023374,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva 4 mRNA,GSM3032160,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva 4 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM3032160,GSM3032160: Larva 4 mRNA; Danio rerio; RNA Seq,GSM3032160,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032160,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,Z4_wt_R2.fastq.gz Z4_wt_R1.fastq.gz,fastq fastq,19775711456.0,159481544.0,GSM3032160 r1,0:26 1:98,A:5483727144;C:4548396363;G:4737957565;T:5002119078;N:3511306,26,98,,,5483727144,4548396363,4737957565,5002119078,3511306,SRX3768857,SRS3023374,SRA623333,GEO,Max Delbrück Center,2,0.00331,0.93006,0.00057,0.05973,0.99253,0.82369,0.38666,0.48899,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Larval,Larval,Trunk,Surface Structure
43999,SRR6811816,SRX3768856,SRS3023373,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva 3 mRNA,GSM3032159,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva 3 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM3032159,GSM3032159: Larva 3 mRNA; Danio rerio; RNA Seq,GSM3032159,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032159,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,Z3_wt_R1.fastq.gz Z3_wt_R2.fastq.gz Z3_wt_R3.fastq.gz,fastq fastq fastq,8016913120.0,50105707.0,GSM3032159 r1,0:130 1:14 2:16,A:2047850756;C:1318672327;G:1403772432;T:1743394108;N:52287,130,14,16,,2047850756,1318672327,1403772432,1743394108,52287,SRX3768856,SRS3023373,SRA623333,GEO,Max Delbrück Center,1,0.87661,,0.06466,,0.86614,,0.53364,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Larval,Larval,Trunk,Surface Structure
44005,SRR6211487,SRX3320762,SRS2626335,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva 2 mRNA,GSM2830057,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva 2 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode  a UMI  and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment  we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode  we counted the number of molecules mapped to each gene  using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t =  K ln1 – k o/K  with t the final number of transcripts  k o the observed UMIs  and K the total number of UMIs possible. As protection against barcode sequencing errors  we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore  we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM2830057,GSM2830057: Larva 2 mRNA; Danio rerio; RNA Seq,GSM2830057,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM2830057,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,Z1_wt_R3.fastq.gz Z1_wt_R2.fastq.gz Z1_wt_R1.fastq.gz,fastq fastq fastq,28368351950.0,232527475.0,GSM2830057 r1,0:98 1:14 2:10,A:6582076349;C:4985163175;G:5131319282;T:6085835988;N:3297756,98,14,10,,6582076349,4985163175,5131319282,6085835988,3297756,SRX3320762,SRS2626335,SRA623333,GEO,Max Delbrück Center,1,0.9378,,0.05825,,0.79687,,0.50342,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2017-10-24,Larval,Larval,Trunk,Surface Structure
44006,SRR6211485,SRX3320760,SRS2626333,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva 1 mRNA,GSM2830056,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva 1 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode  a UMI  and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment  we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode  we counted the number of molecules mapped to each gene  using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t =  K ln1 – k o/K  with t the final number of transcripts  k o the observed UMIs  and K the total number of UMIs possible. As protection against barcode sequencing errors  we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore  we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM2830056,GSM2830056: Larva 1 mRNA; Danio rerio; RNA Seq,GSM2830056,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM2830056,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,Z2_1_wt_R1.fastq.gz Z2_1_wt_R2.fastq.gz Z2_1_wt_R3.fastq.gz,fastq fastq fastq,36065037280.0,225406483.0,GSM2830056 r1,0:130 1:14 2:16,A:9121762570;C:5889322717;G:6251660049;T:8039869338;N:228116,130,14,16,,9121762570,5889322717,6251660049,8039869338,228116,SRX3320760,SRS2626333,SRA623333,GEO,Max Delbrück Center,1,0.88569,,0.08353,,0.86016,,0.53379,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2017-10-24,Larval,Larval,Trunk,Surface Structure
44007,SRR6211486,SRX3320760,SRS2626333,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva 1 mRNA,GSM2830056,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva 1 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode  a UMI  and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment  we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode  we counted the number of molecules mapped to each gene  using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t =  K ln1 – k o/K  with t the final number of transcripts  k o the observed UMIs  and K the total number of UMIs possible. As protection against barcode sequencing errors  we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore  we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM2830056,GSM2830056: Larva 1 mRNA; Danio rerio; RNA Seq,GSM2830056,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM2830056,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,Z2_2_wt_R1.fastq.gz Z2_2_wt_R2.fastq.gz Z2_2_wt_R3.fastq.gz,fastq fastq fastq,7700646560.0,48129041.0,GSM2830056 r2,0:130 1:14 2:16,A:1890861891;C:1307860042;G:1403340071;T:1654667424;N:45902,130,14,16,,1890861891,1307860042,1403340071,1654667424,45902,SRX3320760,SRS2626333,SRA623333,GEO,Max Delbrück Center,1,0.89198,,0.07477,,0.87288,,0.49519,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2017-10-24,Larval,Larval,Trunk,Surface Structure
52209,SRR8992787,SRX5771765,SRS4705624,SRP194294,PRJNA540521,Fate plasticity and reprogramming in genetically distinct populations of Danio leucophores,GSE130526,Other,Understanding genetic and cellular bases of adult form remains a fundamental goal at the intersection of developmental and evolutionary biology. The skin pigment cells of vertebrates  derived from embryonic neural crest  are a useful system for elucidating mechanisms of fate specification  pattern formation  and how particular phenotypes impact organismal behavior and ecology. In a survey of Danio fishes  including zebrafish Danio rerio  we identified two populations of white pigment cells—leucophores—one of which arises by transdifferentiation of adult melanophores and another that develops from a yellow/orange xanthophore like progenitor. Single cell transcriptomic  mutational  chemical and ultrastructural analyses of zebrafish leucophores revealed cell type specific chemical compositions  organelle configurations and genetic requirements. At the organismal level  we identified distinct physiological responses of leucophores during environmental background matching and we show that leucophore complement influences behavior. Together  our studies revealed new  independently arisen pigment cell types and mechanisms of fate acquisition in zebrafish  and illustrate how concerted analyses across hierarchical levels can provide insights into phenotypes and their evolution. Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform using zebrafish fin pigment cells FACs sorted for mCherry. For additional details see associated publication,,pubmed:31138706,,Zebrafish fin pigment cells,GSM3741778,,tissue:Dorsal and anal fins|cell type:pigment cells|treatment:Untreated,Zebrafish fin pigment cells,Expression matrix files were generated using cellranger 10X genomics version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Genome build: GRCz11/danRer11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,Dorsal and anal fins,Fins were amputated from fish expressing both pnp4a:palmmCherry and tyrp1b:palmmCherry. To approximately normalize capture of relevant cell types by quantity and improve the likelihood of recovering cells at intermediate states of differentiation  we extracted distal dorsal fin regions 10 mm standard length  SL; n=20 and proximal interstripe anal fin regions 14 mm SL; n=10. Tissue was enzymatically dissociated with Liberase 0.25 mg/mL in dPBS at 25°C for 15 min followed by manual trituration with a flame polished glass pipette for 5 min. Cell suspensions were then filtered through a 70 μm Nylon cell strainer to obtain a single cell suspension. Liberated cells were re suspended in 1% BSA / 5% FBS in dPBS and DAPI 0.1 μg/mL  15 min before FACS purification. All plastic and glass surfaces of cell contact were coated with 1% BSA in dPBS before to use. Prior to sorting for fluorescence levels  single cells were isolated by sequentially gating cells according to their SSC A vs. FSC A  FSC H vs FSC W and SSC H vs SSC W profiles according to standard flow cytometry practices. Cells with high levels of DAPI staining were excluded as dead or damaged. Cells from wild type zebrafish were used as negative control to determine gates for detection of mCherry and GFP fluorescence  and then cells from transgenic fish were purified according to these gates. All samples were kept on ice  except during Liberase incubation  and then sorted chilled.,10X genomics V1 protocol following manufacturer recommendations.,Fish were maintained at 28.5C with 10 h : 14 h light:dark conditions. Larvae were reared with marine rotifers supplemented with Artemac Aquafauna followed by Artemia and flake food. Adults were maintained on Artemia and flake food. Fish stocks of Danio rerio: WTABb  a derivative of inbred ABwp  Tgtyrp1b:palm mCherrywp.rt11  Tgpnp4a:palmmCherrywp.rt10,cell type:pigment cells|treatment:Untreated,GSM3741778,GSM3741778: Zebrafish fin pigment cells; Danio rerio; RNA Seq,GSM3741778,,1,10X genomics V1 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP194294,,,leucophore_S9_L003_R2_001.fastq.gz leucophore_S9_L004_R1_001.fastq.gz,fastq fastq,424061944.0,10241510.0,GSM3741778 r1,0:26 1:57,A:119042142;C:89897538;G:98172861;T:116716009;N:233394,26,57,,,119042142,89897538,98172861,116716009,233394,SRX5771765,SRS4705624,SRA881136,GEO,"Parichy Lab, Biology, University of Washington",1,0.33934,,0.07693,,0.8742,,0.51425,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-04-30,Multi-stage,Multi-stage,Fin,Surface Structure
52244,SRR9050631,SRX5827022,SRS4754836,SRP198298,PRJNA542704,Thyroid hormone regulates distinct paths to maturation in pigment cell lineages,GSE131136,Transcriptome Analysis,Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted  Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.,,pubmed:31140974;pubmed:33933422,,Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 7,GSM3764578,,tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:2650 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid,Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 7,Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,sox10:Cre+ cells from post embryonic zebrafish trunk tissue,Transgenic zebrafish  Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia  rotifers enriched with TH free Algamac Aquafauna  and bloodworms.,cell type:2650 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid,GSM3764578,GSM3764578: Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 7; Danio rerio; RNA Seq,GSM3764578,,1,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP198298,,dangling references:treat as unmapped,hypo5_possorted_genome_bam.bam,10X Genomics bam file,6174558858.0,108325594.0,GSM3764578 r1,0:57,A:1897524564;C:1180297377;G:1360942367;T:1732425907;N:3368643,57,,,,1897524564,1180297377,1360942367,1732425907,3368643,SRX5827022,SRS4754836,SRA886020,GEO,"Biology, University of Virginia",1,0.91289,,0.25388,,0.82856,,0.50847,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-05-13,Larval,Larval,Trunk,Surface Structure
52245,SRR9050630,SRX5827021,SRS4754835,SRP198298,PRJNA542704,Thyroid hormone regulates distinct paths to maturation in pigment cell lineages,GSE131136,Transcriptome Analysis,Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted  Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.,,pubmed:31140974;pubmed:33933422,,Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 6,GSM3764577,,tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:1888 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid,Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 6,Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,sox10:Cre+ cells from post embryonic zebrafish trunk tissue,Transgenic zebrafish  Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia  rotifers enriched with TH free Algamac Aquafauna  and bloodworms.,cell type:1888 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid,GSM3764577,GSM3764577: Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 6; Danio rerio; RNA Seq,GSM3764577,,1,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP198298,,dangling references:treat as unmapped,hypo4_possorted_genome_bam.bam,10X Genomics bam file,4410277587.0,77373291.0,GSM3764577 r1,0:57,A:1320513576;C:874241368;G:1044266437;T:1169033783;N:2222423,57,,,,1320513576,874241368,1044266437,1169033783,2222423,SRX5827021,SRS4754835,SRA886020,GEO,"Biology, University of Virginia",1,0.92536,,0.20155,,0.83473,,0.50983,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-05-13,Larval,Larval,Trunk,Surface Structure
52246,SRR9050629,SRX5827020,SRS4754834,SRP198298,PRJNA542704,Thyroid hormone regulates distinct paths to maturation in pigment cell lineages,GSE131136,Transcriptome Analysis,Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted  Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.,,pubmed:31140974;pubmed:33933422,,Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 5,GSM3764576,,tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:774 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid,Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 5,Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,sox10:Cre+ cells from post embryonic zebrafish trunk tissue,Transgenic zebrafish  Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia  rotifers enriched with TH free Algamac Aquafauna  and bloodworms.,cell type:774 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid,GSM3764576,GSM3764576: Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 5; Danio rerio; RNA Seq,GSM3764576,,1,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP198298,,dangling references:treat as unmapped,hypo3_possorted_genome_bam.bam,10X Genomics bam file,8444232738.0,148144434.0,GSM3764576 r1,0:57,A:2380116568;C:1626615273;G:2248860789;T:2185343861;N:3296247,57,,,,2380116568,1626615273,2248860789,2185343861,3296247,SRX5827020,SRS4754834,SRA886020,GEO,"Biology, University of Virginia",1,0.91177,,0.16393,,0.80509,,0.514,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-05-13,Larval,Larval,Trunk,Surface Structure
52247,SRR9050628,SRX5827019,SRS4754833,SRP198298,PRJNA542704,Thyroid hormone regulates distinct paths to maturation in pigment cell lineages,GSE131136,Transcriptome Analysis,Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted  Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.,,pubmed:31140974;pubmed:33933422,,Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 4,GSM3764575,,tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:941 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid,Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 4,Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,sox10:Cre+ cells from post embryonic zebrafish trunk tissue,Transgenic zebrafish  Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia  rotifers enriched with TH free Algamac Aquafauna  and bloodworms.,cell type:941 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid,GSM3764575,GSM3764575: Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 4; Danio rerio; RNA Seq,GSM3764575,,1,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP198298,,dangling references:treat as unmapped,hypo2_possorted_genome_bam.bam,10X Genomics bam file,8711801454.0,152838622.0,GSM3764575 r1,0:57,A:2469579044;C:1654897730;G:2303443265;T:2280478208;N:3403207,57,,,,2469579044,1654897730,2303443265,2280478208,3403207,SRX5827019,SRS4754833,SRA886020,GEO,"Biology, University of Virginia",1,0.90749,,0.17908,,0.8017,,0.5124,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-05-13,Larval,Larval,Trunk,Surface Structure
52248,SRR9050627,SRX5827018,SRS4754832,SRP198298,PRJNA542704,Thyroid hormone regulates distinct paths to maturation in pigment cell lineages,GSE131136,Transcriptome Analysis,Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted  Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.,,pubmed:31140974;pubmed:33933422,,Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 3,GSM3764574,,tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:1073 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid,Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 3,Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,sox10:Cre+ cells from post embryonic zebrafish trunk tissue,Transgenic zebrafish  Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia  rotifers enriched with TH free Algamac Aquafauna  and bloodworms.,cell type:1073 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid,GSM3764574,GSM3764574: Neural crest derived cells from hypothyroid  post embryonic zebrafish trunks  biological replicate 3; Danio rerio; RNA Seq,GSM3764574,,1,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP198298,,dangling references:treat as unmapped,hypo1_possorted_genome_bam.bam,10X Genomics bam file,15530826765.0,272470645.0,GSM3764574 r1,0:57,A:4458931221;C:3243678800;G:3916155957;T:3908839406;N:3221381,57,,,,4458931221,3243678800,3916155957,3908839406,3221381,SRX5827018,SRS4754832,SRA886020,GEO,"Biology, University of Virginia",1,0.94166,,0.13327,,0.79304,,0.49472,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-05-13,Larval,Larval,Trunk,Surface Structure
52249,SRR9050626,SRX5827017,SRS4754831,SRP198298,PRJNA542704,Thyroid hormone regulates distinct paths to maturation in pigment cell lineages,GSE131136,Transcriptome Analysis,Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted  Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.,,pubmed:31140974;pubmed:33933422,,Neural crest derived cells from hypothyroid  post embryonic zebrafish skins  biological replicate 2,GSM3764573,,tissue:sox10:Cre+ cells from post embryonic zebrafish skin tissue|cell type:3033 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid,Neural crest derived cells from hypothyroid  post embryonic zebrafish skins  biological replicate 2,Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,sox10:Cre+ cells from post embryonic zebrafish skin tissue,Transgenic zebrafish  Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia  rotifers enriched with TH free Algamac Aquafauna  and bloodworms.,cell type:3033 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid,GSM3764573,GSM3764573: Neural crest derived cells from hypothyroid  post embryonic zebrafish skins  biological replicate 2; Danio rerio; RNA Seq,GSM3764573,,1,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP198298,,dangling references:treat as unmapped,hypo6_possorted_genome_bam.bam,10X Genomics bam file,7642585251.0,134080443.0,GSM3764573 r1,0:57,A:2330102138;C:1530481079;G:1741129436;T:2036914417;N:3958181,57,,,,2330102138,1530481079,1741129436,2036914417,3958181,SRX5827017,SRS4754831,SRA886020,GEO,"Biology, University of Virginia",1,0.92859,,0.20322,,0.83019,,0.51386,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-05-13,Larval,Larval,Skin,Surface Structure
52250,SRR9050625,SRX5827016,SRS4754830,SRP198298,PRJNA542704,Thyroid hormone regulates distinct paths to maturation in pigment cell lineages,GSE131136,Transcriptome Analysis,Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted  Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.,,pubmed:31140974;pubmed:33933422,,Neural crest derived cells from hypothyroid  juvenile zebrafish trunks  biological replicate 1,GSM3764572,,tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:2135 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 11 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid,Neural crest derived cells from hypothyroid  juvenile zebrafish trunks  biological replicate 1,Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,sox10:Cre+ cells from post embryonic zebrafish trunk tissue,Transgenic zebrafish  Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia  rotifers enriched with TH free Algamac Aquafauna  and bloodworms.,cell type:2135 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 11 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid,GSM3764572,GSM3764572: Neural crest derived cells from hypothyroid  juvenile zebrafish trunks  biological replicate 1; Danio rerio; RNA Seq,GSM3764572,,1,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP198298,,dangling references:treat as unmapped,hypo7_possorted_genome_bam.bam,10X Genomics bam file,5078170983.0,89090719.0,GSM3764572 r1,0:57,A:1526791201;C:989860604;G:1192544480;T:1366270035;N:2704663,57,,,,1526791201,989860604,1192544480,1366270035,2704663,SRX5827016,SRS4754830,SRA886020,GEO,"Biology, University of Virginia",1,0.92899,,0.25348,,0.83571,,0.48794,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-05-13,Multi-stage,Multi-stage,Trunk,Surface Structure
52251,SRR9050624,SRX5827015,SRS4754829,SRP198298,PRJNA542704,Thyroid hormone regulates distinct paths to maturation in pigment cell lineages,GSE131136,Transcriptome Analysis,Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted  Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.,,pubmed:31140974;pubmed:33933422,,Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 6,GSM3764571,,tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:2384 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish|treatment:Euthyroid,Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 6,Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,sox10:Cre+ cells from post embryonic zebrafish trunk tissue,Transgenic zebrafish  Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia  rotifers enriched with TH free Algamac Aquafauna  and bloodworms.,cell type:2384 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish|treatment:Euthyroid,GSM3764571,GSM3764571: Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 6; Danio rerio; RNA Seq,GSM3764571,,1,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP198298,,dangling references:treat as unmapped,eu4_possorted_genome_bam.bam,10X Genomics bam file,5411416524.0,94937132.0,GSM3764571 r1,0:57,A:1638197208;C:1052881199;G:1241396499;T:1476057783;N:2883835,57,,,,1638197208,1052881199,1241396499,1476057783,2883835,SRX5827015,SRS4754829,SRA886020,GEO,"Biology, University of Virginia",1,0.91678,,0.23274,,0.83435,,0.51765,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-05-13,Larval,Larval,Trunk,Surface Structure
52252,SRR9050623,SRX5827014,SRS4754828,SRP198298,PRJNA542704,Thyroid hormone regulates distinct paths to maturation in pigment cell lineages,GSE131136,Transcriptome Analysis,Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted  Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.,,pubmed:31140974;pubmed:33933422,,Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 5,GSM3764570,,tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:807 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish|treatment:Euthyroid,Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 5,Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,sox10:Cre+ cells from post embryonic zebrafish trunk tissue,Transgenic zebrafish  Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia  rotifers enriched with TH free Algamac Aquafauna  and bloodworms.,cell type:807 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish|treatment:Euthyroid,GSM3764570,GSM3764570: Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 5; Danio rerio; RNA Seq,GSM3764570,,1,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP198298,,dangling references:treat as unmapped,eu3_possorted_genome_bam.bam,10X Genomics bam file,8326974105.0,146087265.0,GSM3764570 r1,0:57,A:2330538697;C:1602893033;G:2265568086;T:2124697512;N:3276777,57,,,,2330538697,1602893033,2265568086,2124697512,3276777,SRX5827014,SRS4754828,SRA886020,GEO,"Biology, University of Virginia",1,0.91032,,0.14841,,0.81207,,0.52798,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-05-13,Larval,Larval,Trunk,Surface Structure
52253,SRR9050622,SRX5827013,SRS4754827,SRP198298,PRJNA542704,Thyroid hormone regulates distinct paths to maturation in pigment cell lineages,GSE131136,Transcriptome Analysis,Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted  Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.,,pubmed:31140974;pubmed:33933422,,Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 4,GSM3764569,,tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:808 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish|treatment:Euthyroid,Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 4,Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,sox10:Cre+ cells from post embryonic zebrafish trunk tissue,Transgenic zebrafish  Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia  rotifers enriched with TH free Algamac Aquafauna  and bloodworms.,cell type:808 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish|treatment:Euthyroid,GSM3764569,GSM3764569: Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 4; Danio rerio; RNA Seq,GSM3764569,,1,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP198298,,dangling references:treat as unmapped,eu2_possorted_genome_bam.bam,10X Genomics bam file,9524985741.0,167105013.0,GSM3764569 r1,0:57,A:2659154932;C:1836434156;G:2596847773;T:2428811653;N:3737227,57,,,,2659154932,1836434156,2596847773,2428811653,3737227,SRX5827013,SRS4754827,SRA886020,GEO,"Biology, University of Virginia",1,0.91042,,0.14492,,0.81148,,0.53287,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-05-13,Larval,Larval,Trunk,Surface Structure
52254,SRR9050621,SRX5827012,SRS4754826,SRP198298,PRJNA542704,Thyroid hormone regulates distinct paths to maturation in pigment cell lineages,GSE131136,Transcriptome Analysis,Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted  Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.,,pubmed:31140974;pubmed:33933422,,Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 3,GSM3764568,,tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:944 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish|treatment:Euthyroid,Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 3,Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,sox10:Cre+ cells from post embryonic zebrafish trunk tissue,Transgenic zebrafish  Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia  rotifers enriched with TH free Algamac Aquafauna  and bloodworms.,cell type:944 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish|treatment:Euthyroid,GSM3764568,GSM3764568: Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 3; Danio rerio; RNA Seq,GSM3764568,,1,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP198298,,dangling references:treat as unmapped,eu1_possorted_genome_bam.bam,10X Genomics bam file,14548569306.0,255238058.0,GSM3764568 r1,0:57,A:4144426475;C:3024945467;G:3685756189;T:3690427238;N:3013937,57,,,,4144426475,3024945467,3685756189,3690427238,3013937,SRX5827012,SRS4754826,SRA886020,GEO,"Biology, University of Virginia",1,0.94033,,0.12393,,0.79338,,0.50069,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-05-13,Larval,Larval,Trunk,Surface Structure
52255,SRR9050620,SRX5827011,SRS4754825,SRP198298,PRJNA542704,Thyroid hormone regulates distinct paths to maturation in pigment cell lineages,GSE131136,Transcriptome Analysis,Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted  Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.,,pubmed:31140974;pubmed:33933422,,Neural crest derived cells from euthyroid  post embryonic zebrafish skins  biological replicate 2,GSM3764567,,tissue:sox10:Cre+ cells from post embryonic zebrafish skin tissue|cell type:3008 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from skins. Zebrafish range in stage from 7.2 10.4 SSL.|treatment:Euthyroid,Neural crest derived cells from euthyroid  post embryonic zebrafish skins  biological replicate 2,Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,sox10:Cre+ cells from post embryonic zebrafish skin tissue,Transgenic zebrafish  Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia  rotifers enriched with TH free Algamac Aquafauna  and bloodworms.,cell type:3008 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from skins. Zebrafish  range in stage from 7.2 10.4 SSL.|treatment:Euthyroid,GSM3764567,GSM3764567: Neural crest derived cells from euthyroid  post embryonic zebrafish skins  biological replicate 2; Danio rerio; RNA Seq,GSM3764567,,1,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP198298,,dangling references:treat as unmapped,eu5_possorted_genome_bam.bam,10X Genomics bam file,7562050749.0,132667557.0,GSM3764567 r1,0:57,A:2291130941;C:1508834109;G:1752506997;T:2005478206;N:4100496,57,,,,2291130941,1508834109,1752506997,2005478206,4100496,SRX5827011,SRS4754825,SRA886020,GEO,"Biology, University of Virginia",1,0.92351,,0.19606,,0.82913,,0.5204,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-05-13,Larval,Larval,Skin,Surface Structure
52256,SRR9050619,SRX5827010,SRS4754824,SRP198298,PRJNA542704,Thyroid hormone regulates distinct paths to maturation in pigment cell lineages,GSE131136,Transcriptome Analysis,Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted  Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.,,pubmed:31140974;pubmed:33933422,,Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 1,GSM3764566,,tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:2168 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Zebrafish were stage 11 SSL stage juvenile.|treatment:Euthyroid,Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 1,Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,sox10:Cre+ cells from post embryonic zebrafish trunk tissue,Transgenic zebrafish  Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia  rotifers enriched with TH free Algamac Aquafauna  and bloodworms.,cell type:2168 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Zebrafish were stage 11 SSL stage juvenile.|treatment:Euthyroid,GSM3764566,GSM3764566: Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 1; Danio rerio; RNA Seq,GSM3764566,,1,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP198298,,dangling references:treat as unmapped,eu6_possorted_genome_bam.bam,10X Genomics bam file,5005233954.0,87811122.0,GSM3764566 r1,0:57,A:1531421605;C:966957285;G:1151579626;T:1352667292;N:2608146,57,,,,1531421605,966957285,1151579626,1352667292,2608146,SRX5827010,SRS4754824,SRA886020,GEO,"Biology, University of Virginia",1,0.92288,,0.25231,,0.83479,,0.5014,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-05-13,Multi-stage,Multi-stage,Trunk,Surface Structure
53593,SRR11886700,SRX8434172,SRS6745285,SRP265421,PRJNA559885,A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration,PRJNA559885,Other,The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities  while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic  developmental  cellular and molecular studies  the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio  we uncovered species specific and evolutionarily conserved genomic responses to amputation.,,,,zebrafish fin regeneration,zebrafish fin 1dpa,,strain:AB|isolate:12|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish blastema single cell,L41598,L41598,The African killifish and zebrafish single cell RNA seq were done with the 10x Chromium platform. About 20 fish were used for cell dissociation in each experiment. Hoechst stained cells 100 000 cells from the dissected blastema tissues at 1dpa were collected on ice using a BD Influx sorter. The viability of cells 94.5% was determined before loading cells into 10x Chromium platform.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP265421,,loader:fastq load.py,L41598_S1_L001_I1_001.fastq.gz L41598_S1_L001_R1_001.fastq.gz L41598_S1_L001_R2_001.fastq.gz L41598_S1_L002_I1_001.fastq.gz L41598_S1_L002_R1_001.fastq.gz L41598_S1_L002_R2_001.fastq.gz L41598_S1_L003_I1_001.fastq.gz L41598_S1_L003_R1_001.fastq.gz L41598_S1_L003_R2_001.fastq.gz L41598_S1_L004_I1_001.fastq.gz L41598_S1_L004_R1_001.fastq.gz L41598_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,52222012142.0,411196946.0,L41598 S1 L001 I1 001.fastq.gz,0:8 1:28 2:91,A:10978857897;C:7760934381;G:8557391299;T:10029401940;N:92336569,8,28,91,,10978857897,7760934381,8557391299,10029401940,92336569,SRX8434172,SRS6745285,SRA1081627,Stowers Institute for Medical Research|Sanchez lab,Stowers Institute for Medical Research,1,0.92629,,0.12539,,0.78589,,0.5225,,91,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2020-08-11,Adult,Adult,Fin,Surface Structure
55221,SRR10182211,SRX6902836,SRS5434733,SRP223244,PRJNA574059,Cellular diversity of the regenerating caudal fin,GSE137971,Transcriptome Analysis,single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies  filtered through 40 µm cell strainers  and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging  alignment to zebrafish reference genome GRCz10  and feature counting based on Ensembl release 91 cellranger count.,,pubmed:32851162,,1dpa fin1 scRNA,GSM4095395,,source name:1dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:1 day post amputation,1dpa fin1 scRNA,All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly  sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.,1dpa caudal fin,,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility  with system water temperature at 28.5˚C  and a day night cycle controlled as 14 hr light/10 hr dark.,strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:1 day post amputation,GSM4095395,GSM4095395: 1dpa fin1 scRNA; Danio rerio; RNA Seq,GSM4095395,,1,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,GEO Accession:GSM4095395,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP223244,,,1dpa1_S1_L002_R1_001.fastq.gz 1dpa1_S1_L002_R2_001.fastq.gz,fastq fastq,3515690517.0,34808817.0,GSM4095395 r1,0:26 1:75,A:1021208515;C:750623954;G:773148636;T:968849435;N:1859977,26,75,,,1021208515,750623954,773148636,968849435,1859977,SRX6902836,SRS5434733,SRA968154,GEO,"Ting Wang, Genetics, Washington University St Louis",2,0.00195,0.91495,0.00089,0.10966,0.99699,0.84855,0.35643,0.59738,26,75,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-09-25,Adult,Adult,Fin,Surface Structure
55222,SRR10182210,SRX6902835,SRS5434732,SRP223244,PRJNA574059,Cellular diversity of the regenerating caudal fin,GSE137971,Transcriptome Analysis,single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies  filtered through 40 µm cell strainers  and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging  alignment to zebrafish reference genome GRCz10  and feature counting based on Ensembl release 91 cellranger count.,,pubmed:32851162,,preinjury fin2 scRNA,GSM4095394,,source name:Preinjury caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury,preinjury fin2 scRNA,All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly  sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.,Preinjury caudal fin,,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility  with system water temperature at 28.5˚C  and a day night cycle controlled as 14 hr light/10 hr dark.,strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury,GSM4095394,GSM4095394: preinjury fin2 scRNA; Danio rerio; RNA Seq,GSM4095394,,1,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,GEO Accession:GSM4095394,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP223244,,,samp2_S2_L002_R2_001.fastq.gz samp2_S2_L002_R1_001.fastq.gz,fastq fastq,14313306001.0,141715901.0,GSM4095394 r1,0:26 1:75,A:4080921082;C:3121900376;G:3341495424;T:3761528384;N:7460735,26,75,,,4080921082,3121900376,3341495424,3761528384,7460735,SRX6902835,SRS5434732,SRA968154,GEO,"Ting Wang, Genetics, Washington University St Louis",2,0.0029,0.89943,0.00115,0.07948,0.99543,0.8714,0.29607,0.47916,26,75,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-09-25,Adult,Adult,Fin,Surface Structure
55223,SRR10182209,SRX6902834,SRS5434731,SRP223244,PRJNA574059,Cellular diversity of the regenerating caudal fin,GSE137971,Transcriptome Analysis,single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies  filtered through 40 µm cell strainers  and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging  alignment to zebrafish reference genome GRCz10  and feature counting based on Ensembl release 91 cellranger count.,,pubmed:32851162,,preinjury fin1 scRNA,GSM4095393,,source name:Preinjury caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury,preinjury fin1 scRNA,All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly  sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.,Preinjury caudal fin,,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility  with system water temperature at 28.5˚C  and a day night cycle controlled as 14 hr light/10 hr dark.,strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury,GSM4095393,GSM4095393: preinjury fin1 scRNA; Danio rerio; RNA Seq,GSM4095393,,1,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,GEO Accession:GSM4095393,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP223244,,,samp1_S1_L001_R1_001.fastq.gz samp1_S1_L001_R2_001.fastq.gz,fastq fastq,14610147425.0,144654925.0,GSM4095393 r1,0:26 1:75,A:4066051353;C:3189039694;G:3388950081;T:3856651906;N:109454391,26,75,,,4066051353,3189039694,3388950081,3856651906,109454391,SRX6902834,SRS5434731,SRA968154,GEO,"Ting Wang, Genetics, Washington University St Louis",2,0.0024,0.87757,0.00072,0.08379,0.99504,0.85269,0.34276,0.52515,26,75,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-09-25,Adult,Adult,Fin,Surface Structure