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
33615,SRR30272850,SRX25733949,SRS22373737,SRP526812,PRJNA1148907,Single cell RNA sequencing to uncover tissue specific transcriptomic changes induced by perfluorooctanesulfonic acid PFOS in larval zebrafish Danio rerio,PRJNA1148907,Other,The aim is to to apply single cell RNA sequencing of zebrafish larvae to identify novel tissue specific mechanisms and processes following embryonic exposure to perfluorooctanesulfonic acid PFOS,,pubmed:39947082,,PFOS  S2,Sample2,,strain:Tgins:GFP zebrafish on an AB wildtype background|age:72 hpf|dev stage:protruding mouth stage|collection date:2023 01 03|geo loc name:USA: Massachusetts|sex:NA|tissue:whole body cells|treatment:PFOS 16 uM|BioSampleModel:Model organism or animal,,,,,,,,,PFOS,PFOS,PFOS,PFOS  S2  scRNAseq,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PCR,PAIRED,ILLUMINA,NextSeq 500,,SRP526812,,,G194-S2-PFOS_S2_L001_R1_001.fastq.gz G194-S2-PFOS_S2_L001_R2_001.fastq.gz G194-S2-PFOS_S2_L002_R1_001.fastq.gz G194-S2-PFOS_S2_L002_R2_001.fastq.gz G194-S2-PFOS_S2_L003_R1_001.fastq.gz G194-S2-PFOS_S2_L003_R2_001.fastq.gz G194-S2-PFOS_S2_L004_R1_001.fastq.gz G194-S2-PFOS_S2_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,21751958340.0,184338630.0,G194 S2 PFOS S2 L001 R1 001.fastq.gz,0:28 1:90,A:6239773453;C:4634671870;G:5196638658;T:5672561386;N:8312973,28,90,,,6239773453,4634671870,5196638658,5672561386,8312973,SRX25733949,SRS22373737,SRA1949185,University of Massachusetts Amherst|Environmental Health Sciences,University of Massachusetts Amherst,2,0.01021,0.92344,0.00451,0.22962,0.99328,0.79847,0.28896,0.51751,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2024-08-16,Larval,Larval,Trunk,Surface Structure
33616,SRR30272851,SRX25733948,SRS22373736,SRP526812,PRJNA1148907,Single cell RNA sequencing to uncover tissue specific transcriptomic changes induced by perfluorooctanesulfonic acid PFOS in larval zebrafish Danio rerio,PRJNA1148907,Other,The aim is to to apply single cell RNA sequencing of zebrafish larvae to identify novel tissue specific mechanisms and processes following embryonic exposure to perfluorooctanesulfonic acid PFOS,,pubmed:39947082,,DMSO  S1,Sample1,,strain:Tgins:GFP zebrafish on an AB wildtype background|age:72 hpf|dev stage:protruding mouth stage|collection date:2023 01 03|geo loc name:USA: Massachusetts|sex:NA|tissue:whole body cells|treatment:DMSO 0.01%|BioSampleModel:Model organism or animal,,,,,,,,,DMSO,DMSO,DMSO,DMSO  S1  scRNAseq,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PCR,PAIRED,ILLUMINA,NextSeq 500,,SRP526812,,,G194-S1-DMSO_S1_L001_R1_001.fastq.gz G194-S1-DMSO_S1_L001_R2_001.fastq.gz G194-S1-DMSO_S1_L002_R1_001.fastq.gz G194-S1-DMSO_S1_L002_R2_001.fastq.gz G194-S1-DMSO_S1_L003_R1_001.fastq.gz G194-S1-DMSO_S1_L003_R2_001.fastq.gz G194-S1-DMSO_S1_L004_R1_001.fastq.gz G194-S1-DMSO_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,21636838838.0,183363041.0,G194 S1 DMSO S1 L001 R1 001.fastq.gz,0:28 1:90,A:6175214014;C:4647929260;G:5248646646;T:5556827078;N:8221840,28,90,,,6175214014,4647929260,5248646646,5556827078,8221840,SRX25733948,SRS22373736,SRA1949185,University of Massachusetts Amherst|Environmental Health Sciences,University of Massachusetts Amherst,2,0.01048,0.92488,0.00455,0.20966,0.99358,0.81464,0.28056,0.57876,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2024-08-16,Larval,Larval,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
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
69558,SRR18901602,SRX14979859,SRS12729750,SRP371883,PRJNA831276,Lipid droplets are a metabolic vulnerability in melanoma,GSE201378,Transcriptome Analysis,Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma,,pubmed:37268606,,TEAZ scRNAseq,GSM6062264,,source name:Skin|tissue:Skin|cell type:melanoma,TEAZ scRNAseq,Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11,Skin,,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,tissue:Skin|cell type:melanoma,GSM6062264,GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq,GSM6062264 r1,GSM6062264,1,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,loader:fastq load.py,2544_PTEN_combined_IGO_11963_4_S2_L001_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L001_R2_001.fastq.gz,fastq fastq,9314576760.0,77621473.0,GSM6062264 r1,0:29 1:91,A:2571624849;C:2103171866;G:2248508025;T:2390911966;N:360054,29,91,,,2571624849,2103171866,2248508025,2390911966,360054,SRX14979859,SRS12729750,SRA1408865,"Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center","Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.00434,0.8777,0.00177,0.14429,0.99253,0.78492,0.35282,0.53036,29,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-04-23,Undetermined,Undetermined,Skin,Surface Structure
69559,SRR18901603,SRX14979859,SRS12729750,SRP371883,PRJNA831276,Lipid droplets are a metabolic vulnerability in melanoma,GSE201378,Transcriptome Analysis,Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma,,pubmed:37268606,,TEAZ scRNAseq,GSM6062264,,source name:Skin|tissue:Skin|cell type:melanoma,TEAZ scRNAseq,Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11,Skin,,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,tissue:Skin|cell type:melanoma,GSM6062264,GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq,GSM6062264 r1,GSM6062264,1,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,loader:fastq load.py,2544_PTEN_combined_IGO_11963_4_S2_L002_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L002_R2_001.fastq.gz,fastq fastq,9122357880.0,76019649.0,GSM6062264 r2,0:29 1:91,A:2521047948;C:2056950129;G:2200048731;T:2343919901;N:391171,29,91,,,2521047948,2056950129,2200048731,2343919901,391171,SRX14979859,SRS12729750,SRA1408865,"Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center","Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.00471,0.87992,0.00196,0.14374,0.99255,0.78476,0.35593,0.54484,29,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-04-23,Undetermined,Undetermined,Skin,Surface Structure
69560,SRR18901604,SRX14979859,SRS12729750,SRP371883,PRJNA831276,Lipid droplets are a metabolic vulnerability in melanoma,GSE201378,Transcriptome Analysis,Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma,,pubmed:37268606,,TEAZ scRNAseq,GSM6062264,,source name:Skin|tissue:Skin|cell type:melanoma,TEAZ scRNAseq,Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11,Skin,,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,tissue:Skin|cell type:melanoma,GSM6062264,GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq,GSM6062264 r1,GSM6062264,1,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,loader:fastq load.py,2544_PTEN_combined_IGO_11963_4_S2_L003_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L003_R2_001.fastq.gz,fastq fastq,9307586160.0,77563218.0,GSM6062264 r3,0:29 1:91,A:2569072609;C:2102732051;G:2247036264;T:2388393636;N:351600,29,91,,,2569072609,2102732051,2247036264,2388393636,351600,SRX14979859,SRS12729750,SRA1408865,"Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center","Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.00429,0.87889,0.00178,0.1429,0.99271,0.78589,0.35728,0.54587,29,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-04-23,Undetermined,Undetermined,Skin,Surface Structure
69561,SRR18901605,SRX14979859,SRS12729750,SRP371883,PRJNA831276,Lipid droplets are a metabolic vulnerability in melanoma,GSE201378,Transcriptome Analysis,Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma,,pubmed:37268606,,TEAZ scRNAseq,GSM6062264,,source name:Skin|tissue:Skin|cell type:melanoma,TEAZ scRNAseq,Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11,Skin,,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,tissue:Skin|cell type:melanoma,GSM6062264,GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq,GSM6062264 r1,GSM6062264,1,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,loader:fastq load.py,2544_PTEN_combined_IGO_11963_4_S2_L004_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L004_R2_001.fastq.gz,fastq fastq,9382270920.0,78185591.0,GSM6062264 r4,0:29 1:91,A:2591803792;C:2116313097;G:2264892157;T:2408930364;N:331510,29,91,,,2591803792,2116313097,2264892157,2408930364,331510,SRX14979859,SRS12729750,SRA1408865,"Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center","Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.00445,0.87912,0.00184,0.14625,0.99287,0.78573,0.37029,0.5207,29,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-04-23,Undetermined,Undetermined,Skin,Surface Structure
70844,SRR20737630,SRX16758028,SRS14385048,SRP389175,PRJNA864829,Single nuclei profiling of chromatin accessibility and transcriptomes of jaw mesenchymal cells in wild type and nr5a2 mutant zebrafish embryos,GSE210251,Other,The functional jaw is composed of multiple connective tissues including skeletal components bone  cartilage  and teeth  tendon  ligament  and musculature. Cranial neural crest derived mesenchyme of the mandibular arch give rise to diverse tissue types within the lower jaw. To understand how the specification of diverse cell types with spatial and temporal precision is achieved  we profile multi omic chromatin accessibility snATACseq and transcriptome snRNAseq of jaw mesenchyme at single cell resolution from the developing zebrafish jaw. Overall design: To profile chromatin accessibility and transcriptome in the same cell from developing jaw  we collected nr5a2:GFP+ jaw mesenchyme from control and nr5a2 mutant zebrafish embryos at 2.5 dpf. The nuclei of FACS GFP+ cells were subjected to single cell profiling and sequencing by the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression platform of 10X Genomics.,,pubmed:36905926,,Multiome mutant nr5a2 GFP 2.5dpf head snRNA seq,GSM6424705,,source name:Jaw mesenchyme|tissue:Jaw mesenchyme|developmental stage:2.5 dpf|genotype:nr5a2:mGFP DBD del/oz3|transgene1:Tgnr5a2:GFP CAAX DBD delel875|transgene2:Tgscxa:mCherryfb301|facs markers:DAPI  / GFP+,Multiome mutant nr5a2 GFP 2.5dpf head snRNA seq,Multi omic libraries of snATACseq and snRNAseq from the same barcoded single nuclei were constructed per manufacturer’s instructions 10X Genomics  Chromium Next GEM Single Cell Multiome ATAC + Gene Expression  protocol CG000338. QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit. Libraries were sequenced on Illumina HiSeq control or NextSeq mutant platforms. For sequencing snATACseq libraries  both Read1 and Read2 were extended to 60 cycles  whereas for sequencing snRNAseq libraries  Read2 was extended to 102 cycles for longer coverage. Sequencing reads were aligned to customized genome built with GRCz11.fa  GRCz11.104.gtf and JASPAR2020.pfm and added GFP CAAX and mCherry gene information. Alignment  peak calling for snATACseq data and cell calling were performed by Cell Ranger ARC v2.0.0 per manufacturer’s instructions 10X Genomics to generate peak by cell and gene by cell count matrices. Assembly: GRCz11 Supplementary files format and content: Each sample has one processed data output by Cell Ranger ARC v2.0.0: peak by cell and gene by cell count matrices in HDF5 format.,Jaw mesenchyme,,Zebrafish embryos are screened for nr5a2:mGFP DBD del+ / scxa:mCherry+ and fin tips are collected for PCR genotyping of oz3 allele mutant and wild type allele control before 2 dpf. Control and mutant heads were decapitated between the eye and ear post anesthesia at 2.5 dpf. Dissected heads twenty heads pre tube were washed twice with fresh and iced Ringer’s solution 116mM NaCl  2.6mM KCl  5mM HEPES  pH 7.0  followed by dissociation at 28.5 °C for 40 min by mechanical   nutating and pipetting every 5 min and enzymatic   in pre warmed protease solution 0.25% trypsin  1 mM EDTA  pH 8.0  and 20 mg/mL Collagenase D from stock of 400 mg/mL Collagenase D in HBSS in PBS until fully dissociated. Dissociation reaction is stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Dissociated cells were collected by centrifugation for 5 min  2000 rpm at 4°C and washed by suspension solution 1% FBS  0.8mM CaCl2  50U/ml Penicillin  0.05mg/ml Streptomycin in Leibovitz Medium twice and filtered by cell strainer before sorting. Live cells were fluorescence activated cell sorted FACS to isolate GFP+ and exclude the cytoplasmic stain Zombie Violet control or nuclear stain DAPI mutant into 0.04% BSA/ PBS at 4°C. Nuclei isolation was performed per manufacturer’s instructions 10X Genomics  protocol CG000169  low cell input protocol with optimalization for zebrafish mesenchyme. FACS cells were pelleted for 15 min  300 rcf at 4oC  and incubated with lysis buffer for 100 s on ice. Isolated nuclei were washed by Wash buffer and Nuclei buffer and checked for nucleus integrity under a fluorescence confocal microscope with DAPI staining before subjected to library construction. To capture accessible chromatin and transcripts from the same cells per manufacturer’s instructions  accessible chromatin regions from isolated nuclei were first targeted and tagged by transposase. Tagged chromatin and ployA mRNA from the same nuclei were pulled down and barcoded with the same sequences within isolated GEMs to achieve single nuclei separation. Chromatin fragments were further indexed with sample specific i7 indexes and linked with Illumina P5 and P7 sequences. Reverse transcription was performed in GEMs to synthesize cDNA from polyA mRNA. cDNAs were further fragmented and indexed with sample specific i7 and i5 indexes and linked with Illumina P5 and P7 sequences. QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit.,All experiments on zebrafish Danio rerio were approved by the Institutional Animal Care and Use Committee of the University of Southern California IACUC protocol #20771 and #21151. Zebrafish are raised in vivarium under standard conditions maintained at 28.5°C with health and water conditions monitored daily.,tissue:Jaw mesenchyme|developmental stage:2.5 dpf|genotype:nr5a2:mGFP DBD del/oz3|transgene1:Tgnr5a2:GFP CAAX DBD delel875|transgene2:Tgscxa:mCherryfb301|facs markers:DAPI  / GFP+,GSM6424705,GSM6424705: Multiome mutant nr5a2 GFP 2.5dpf head snRNA seq; Danio rerio; RNA Seq,GSM6424705 r1,GSM6424705,1,Zebrafish embryos are screened for nr5a2:mGFP DBD del+ / scxa:mCherry+ and fin tips are collected for PCR genotyping of oz3 allele mutant and wild type allele control before 2 dpf. Control and mutant heads were decapitated between the eye and ear post anesthesia at 2.5 dpf. Dissected heads twenty heads pre tube were washed twice with fresh and iced Ringer's solution 116mM NaCl  2.6mM KCl  5mM HEPES  pH 7.0  followed by dissociation at 28.5 °C for 40 min by mechanical   nutating and pipetting every 5 min and enzymatic   in pre warmed protease solution 0.25% trypsin  1 mM EDTA  pH 8.0  and 20 mg/mL Collagenase D from stock of 400 mg/mL Collagenase D in HBSS in PBS until fully dissociated. Dissociation reaction is stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Dissociated cells were collected by centrifugation for 5 min  2000 rpm at 4°C and washed by suspension solution 1% FBS  0.8mM CaCl2  50U/ml Penicillin  0.05mg/ml Streptomycin in Leibovitz Medium twice and filtered by cell strainer before sorting. Live cells were fluorescence activated cell sorted FACS to isolate GFP+ and exclude the cytoplasmic stain Zombie Violet control or nuclear stain DAPI mutant into 0.04% BSA/ PBS at 4°C. Nuclei isolation was performed per manufacturer's instructions 10X Genomics  protocol CG000169  low cell input protocol with optimalization for zebrafish mesenchyme. FACS cells were pelleted for 15 min  300 rcf at 4oC  and incubated with lysis buffer for 100 s on ice. Isolated nuclei were washed by Wash buffer and Nuclei buffer and checked for nucleus integrity under a fluorescence confocal microscope with DAPI staining before subjected to library construction. To capture accessible chromatin and transcripts from the same cells per manufacturer's instructions  accessible chromatin regions from isolated nuclei were first targeted and tagged by transposase. Tagged chromatin and ployA mRNA from the same nuclei were pulled down and barcoded with the same sequences within isolated GEMs to achieve single nuclei separation. Chromatin fragments were further indexed with sample specific i7 indexes and linked with Illumina P5 and P7 sequences. Reverse transcription was performed in GEMs to synthesize cDNA from polyA mRNA. cDNAs were further fragmented and indexed with sample specific i7 and i5 indexes and linked with Illumina P5 and P7 sequences. QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP389175,,loader:fastq load.py,Multiome_mutant_nr5a2_GFP_2.5dpf_head_RNA_S1_L001_R1_001.fastq.gz Multiome_mutant_nr5a2_GFP_2.5dpf_head_RNA_S1_L001_R2_001.fastq.gz,fastq fastq,24616183454.0,187429180.0,GSM6424705 r1,0:29 1:102.34,A:5661562219;C:4278027880;G:4357175731;T:5550818399;N:4768599225,29,102,,,5661562219,4278027880,4357175731,5550818399,4768599225,SRX16758028,SRS14385048,SRA1467000,Stem Cell Department at USC,Stem Cell Department at USC,2,0.01084,0.91331,0.00616,0.27551,0.99153,0.84447,0.51001,0.63176,29,102,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2022-08-01,Hatching,Embryo,Jaw,Surface Structure
70845,SRR20737632,SRX16758026,SRS14385046,SRP389175,PRJNA864829,Single nuclei profiling of chromatin accessibility and transcriptomes of jaw mesenchymal cells in wild type and nr5a2 mutant zebrafish embryos,GSE210251,Other,The functional jaw is composed of multiple connective tissues including skeletal components bone  cartilage  and teeth  tendon  ligament  and musculature. Cranial neural crest derived mesenchyme of the mandibular arch give rise to diverse tissue types within the lower jaw. To understand how the specification of diverse cell types with spatial and temporal precision is achieved  we profile multi omic chromatin accessibility snATACseq and transcriptome snRNAseq of jaw mesenchyme at single cell resolution from the developing zebrafish jaw. Overall design: To profile chromatin accessibility and transcriptome in the same cell from developing jaw  we collected nr5a2:GFP+ jaw mesenchyme from control and nr5a2 mutant zebrafish embryos at 2.5 dpf. The nuclei of FACS GFP+ cells were subjected to single cell profiling and sequencing by the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression platform of 10X Genomics.,,pubmed:36905926,,Multiome control nr5a2 GFP 2.5dpf head snRNA seq,GSM6424703,,source name:Jaw mesenchyme|tissue:Jaw mesenchyme|developmental stage:2.5 dpf|genotype:nr5a2:mGFP DBD del/+|transgene1:Tgnr5a2:GFP CAAX DBD delel875|transgene2:Tgscxa:mCherryfb301|facs markers:Zombie  / GFP+,Multiome control nr5a2 GFP 2.5dpf head snRNA seq,Multi omic libraries of snATACseq and snRNAseq from the same barcoded single nuclei were constructed per manufacturer’s instructions 10X Genomics  Chromium Next GEM Single Cell Multiome ATAC + Gene Expression  protocol CG000338. QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit. Libraries were sequenced on Illumina HiSeq control or NextSeq mutant platforms. For sequencing snATACseq libraries  both Read1 and Read2 were extended to 60 cycles  whereas for sequencing snRNAseq libraries  Read2 was extended to 102 cycles for longer coverage. Sequencing reads were aligned to customized genome built with GRCz11.fa  GRCz11.104.gtf and JASPAR2020.pfm and added GFP CAAX and mCherry gene information. Alignment  peak calling for snATACseq data and cell calling were performed by Cell Ranger ARC v2.0.0 per manufacturer’s instructions 10X Genomics to generate peak by cell and gene by cell count matrices. Assembly: GRCz11 Supplementary files format and content: Each sample has one processed data output by Cell Ranger ARC v2.0.0: peak by cell and gene by cell count matrices in HDF5 format.,Jaw mesenchyme,,Zebrafish embryos are screened for nr5a2:mGFP DBD del+ / scxa:mCherry+ and fin tips are collected for PCR genotyping of oz3 allele mutant and wild type allele control before 2 dpf. Control and mutant heads were decapitated between the eye and ear post anesthesia at 2.5 dpf. Dissected heads twenty heads pre tube were washed twice with fresh and iced Ringer’s solution 116mM NaCl  2.6mM KCl  5mM HEPES  pH 7.0  followed by dissociation at 28.5 °C for 40 min by mechanical   nutating and pipetting every 5 min and enzymatic   in pre warmed protease solution 0.25% trypsin  1 mM EDTA  pH 8.0  and 20 mg/mL Collagenase D from stock of 400 mg/mL Collagenase D in HBSS in PBS until fully dissociated. Dissociation reaction is stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Dissociated cells were collected by centrifugation for 5 min  2000 rpm at 4°C and washed by suspension solution 1% FBS  0.8mM CaCl2  50U/ml Penicillin  0.05mg/ml Streptomycin in Leibovitz Medium twice and filtered by cell strainer before sorting. Live cells were fluorescence activated cell sorted FACS to isolate GFP+ and exclude the cytoplasmic stain Zombie Violet control or nuclear stain DAPI mutant into 0.04% BSA/ PBS at 4°C. Nuclei isolation was performed per manufacturer’s instructions 10X Genomics  protocol CG000169  low cell input protocol with optimalization for zebrafish mesenchyme. FACS cells were pelleted for 15 min  300 rcf at 4oC  and incubated with lysis buffer for 100 s on ice. Isolated nuclei were washed by Wash buffer and Nuclei buffer and checked for nucleus integrity under a fluorescence confocal microscope with DAPI staining before subjected to library construction. To capture accessible chromatin and transcripts from the same cells per manufacturer’s instructions  accessible chromatin regions from isolated nuclei were first targeted and tagged by transposase. Tagged chromatin and ployA mRNA from the same nuclei were pulled down and barcoded with the same sequences within isolated GEMs to achieve single nuclei separation. Chromatin fragments were further indexed with sample specific i7 indexes and linked with Illumina P5 and P7 sequences. Reverse transcription was performed in GEMs to synthesize cDNA from polyA mRNA. cDNAs were further fragmented and indexed with sample specific i7 and i5 indexes and linked with Illumina P5 and P7 sequences. QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit.,All experiments on zebrafish Danio rerio were approved by the Institutional Animal Care and Use Committee of the University of Southern California IACUC protocol #20771 and #21151. Zebrafish are raised in vivarium under standard conditions maintained at 28.5°C with health and water conditions monitored daily.,tissue:Jaw mesenchyme|developmental stage:2.5 dpf|genotype:nr5a2:mGFP DBD del/+|transgene1:Tgnr5a2:GFP CAAX DBD delel875|transgene2:Tgscxa:mCherryfb301|facs markers:Zombie  / GFP+,GSM6424703,GSM6424703: Multiome control nr5a2 GFP 2.5dpf head snRNA seq; Danio rerio; RNA Seq,GSM6424703 r1,GSM6424703,1,Zebrafish embryos are screened for nr5a2:mGFP DBD del+ / scxa:mCherry+ and fin tips are collected for PCR genotyping of oz3 allele mutant and wild type allele control before 2 dpf. Control and mutant heads were decapitated between the eye and ear post anesthesia at 2.5 dpf. Dissected heads twenty heads pre tube were washed twice with fresh and iced Ringer's solution 116mM NaCl  2.6mM KCl  5mM HEPES  pH 7.0  followed by dissociation at 28.5 °C for 40 min by mechanical   nutating and pipetting every 5 min and enzymatic   in pre warmed protease solution 0.25% trypsin  1 mM EDTA  pH 8.0  and 20 mg/mL Collagenase D from stock of 400 mg/mL Collagenase D in HBSS in PBS until fully dissociated. Dissociation reaction is stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Dissociated cells were collected by centrifugation for 5 min  2000 rpm at 4°C and washed by suspension solution 1% FBS  0.8mM CaCl2  50U/ml Penicillin  0.05mg/ml Streptomycin in Leibovitz Medium twice and filtered by cell strainer before sorting. Live cells were fluorescence activated cell sorted FACS to isolate GFP+ and exclude the cytoplasmic stain Zombie Violet control or nuclear stain DAPI mutant into 0.04% BSA/ PBS at 4°C. Nuclei isolation was performed per manufacturer's instructions 10X Genomics  protocol CG000169  low cell input protocol with optimalization for zebrafish mesenchyme. FACS cells were pelleted for 15 min  300 rcf at 4oC  and incubated with lysis buffer for 100 s on ice. Isolated nuclei were washed by Wash buffer and Nuclei buffer and checked for nucleus integrity under a fluorescence confocal microscope with DAPI staining before subjected to library construction. To capture accessible chromatin and transcripts from the same cells per manufacturer's instructions  accessible chromatin regions from isolated nuclei were first targeted and tagged by transposase. Tagged chromatin and ployA mRNA from the same nuclei were pulled down and barcoded with the same sequences within isolated GEMs to achieve single nuclei separation. Chromatin fragments were further indexed with sample specific i7 indexes and linked with Illumina P5 and P7 sequences. Reverse transcription was performed in GEMs to synthesize cDNA from polyA mRNA. cDNAs were further fragmented and indexed with sample specific i7 and i5 indexes and linked with Illumina P5 and P7 sequences. QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP389175,,loader:fastq load.py,Multiome_control_nr5a2_GFP_2.5dpf_head_RNA_S4_L001_R1_001.fastq.gz Multiome_control_nr5a2_GFP_2.5dpf_head_RNA_S4_L001_R2_001.fastq.gz,fastq fastq,64154124610.0,487905462.0,GSM6424703 r1,0:29 1:102.49,A:18612889696;C:13758862487;G:13948126717;T:17774530698;N:59715012,29,102,,,18612889696,13758862487,13948126717,17774530698,59715012,SRX16758026,SRS14385046,SRA1467000,Stem Cell Department at USC,Stem Cell Department at USC,2,0.01181,0.86488,0.00641,0.29997,0.99093,0.80795,0.50941,0.6767,29,102,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2022-08-01,Hatching,Embryo,Jaw,Surface Structure
70967,SRR21007395,SRX17024129,SRS14609022,SRP390913,PRJNA868351,Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [scRNA seq],GSE210941,Transcriptome Analysis,Investigate the role of miR128 in the EHT process and the formation of nHSPCs Overall design: Comparative gene expression  analysis of RNA seq data for WT and MT samples for miRNA128 in Human and Fish,parent bioproject:PRJNA868347,pubmed:37460694,,gRNA jag1  26HPF  scRNAseq,GSM6443156,,source name:trunk tissue containing the AGM|cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF|geo loc name:missing|collection date:missing,gRNA jag1  26HPF  scRNAseq,The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: Tab separated values files and matrix files,trunk tissue containing the AGM,,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b g3’UTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF,GSM6443156,GSM6443156: gRNA jag1  26HPF  scRNAseq; Danio rerio; RNA Seq,GSM6443156 r1,GSM6443156,1,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b gthree primeUTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP390913,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=jag1b DRT S3 L003 I1 001.fastq.gz   read2PairFiles=jag1b DRT S3 L003 R1 001.fastq.gz   read3PairFiles=jag1b DRT S3 L003 R2 001.fastq.gz,jag1b_DRT_S3_L003_I1_001.fastq.gz jag1b_DRT_S3_L003_R1_001.fastq.gz jag1b_DRT_S3_L003_R2_001.fastq.gz,fastq fastq fastq,16114282986.0,126884118.0,GSM6443156 r1,0:8 1:28 2:91,A:4274223175;C:3328097087;G:3589117645;T:3907323607;N:448528,8,28,91,,4274223175,3328097087,3589117645,3907323607,448528,SRX17024129,SRS14609022,SRA1473366,"Nicoli Lab, Genetics/Internal Medicine, Yale University","Nicoli Lab, Genetics/Internal Medicine, Yale University",2,0.00772,0.88765,0.00298,0.21848,0.98776,0.7934,0.36184,0.53575,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-08-10,Pharyngula,Embryo,Trunk,Surface Structure
70968,SRR21007396,SRX17024129,SRS14609022,SRP390913,PRJNA868351,Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [scRNA seq],GSE210941,Transcriptome Analysis,Investigate the role of miR128 in the EHT process and the formation of nHSPCs Overall design: Comparative gene expression  analysis of RNA seq data for WT and MT samples for miRNA128 in Human and Fish,parent bioproject:PRJNA868347,pubmed:37460694,,gRNA jag1  26HPF  scRNAseq,GSM6443156,,source name:trunk tissue containing the AGM|cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF|geo loc name:missing|collection date:missing,gRNA jag1  26HPF  scRNAseq,The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: Tab separated values files and matrix files,trunk tissue containing the AGM,,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b g3’UTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF,GSM6443156,GSM6443156: gRNA jag1  26HPF  scRNAseq; Danio rerio; RNA Seq,GSM6443156 r1,GSM6443156,1,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b gthree primeUTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP390913,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=jag1b DRT S3 L004 I1 001.fastq.gz   read2PairFiles=jag1b DRT S3 L004 R1 001.fastq.gz   read3PairFiles=jag1b DRT S3 L004 R2 001.fastq.gz,jag1b_DRT_S3_L004_I1_001.fastq.gz jag1b_DRT_S3_L004_R1_001.fastq.gz jag1b_DRT_S3_L004_R2_001.fastq.gz,fastq fastq fastq,16084657188.0,126650844.0,GSM6443156 r2,0:8 1:28 2:91,A:4267990504;C:3319270032;G:3579390545;T:3904256142;N:543213,8,28,91,,4267990504,3319270032,3579390545,3904256142,543213,SRX17024129,SRS14609022,SRA1473366,"Nicoli Lab, Genetics/Internal Medicine, Yale University","Nicoli Lab, Genetics/Internal Medicine, Yale University",2,0.00747,0.8896,0.00283,0.21781,0.98778,0.79263,0.36736,0.53802,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-08-10,Pharyngula,Embryo,Trunk,Surface Structure
70969,SRR21007397,SRX17024128,SRS14609021,SRP390913,PRJNA868351,Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [scRNA seq],GSE210941,Transcriptome Analysis,Investigate the role of miR128 in the EHT process and the formation of nHSPCs Overall design: Comparative gene expression  analysis of RNA seq data for WT and MT samples for miRNA128 in Human and Fish,parent bioproject:PRJNA868347,pubmed:37460694,,gRNA csnk1  26HPF  scRNAseq,GSM6443155,,source name:trunk tissue containing the AGM|cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF|geo loc name:missing|collection date:missing,gRNA csnk1  26HPF  scRNAseq,The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: Tab separated values files and matrix files,trunk tissue containing the AGM,,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b g3’UTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF,GSM6443155,GSM6443155: gRNA csnk1  26HPF  scRNAseq; Danio rerio; RNA Seq,GSM6443155 r1,GSM6443155,1,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b gthree primeUTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP390913,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=csnk1a DRT S2 L003 I1 001.fastq.gz   read2PairFiles=csnk1a DRT S2 L003 R1 001.fastq.gz   read3PairFiles=csnk1a DRT S2 L003 R2 001.fastq.gz,csnk1a_DRT_S2_L003_I1_001.fastq.gz csnk1a_DRT_S2_L003_R1_001.fastq.gz csnk1a_DRT_S2_L003_R2_001.fastq.gz,fastq fastq fastq,17585727973.0,138470299.0,GSM6443155 r1,0:8 1:28 2:91,A:4685099762;C:3662694223;G:3795199750;T:4334481609;N:490237,8,28,91,,4685099762,3662694223,3795199750,4334481609,490237,SRX17024128,SRS14609021,SRA1473366,"Nicoli Lab, Genetics/Internal Medicine, Yale University","Nicoli Lab, Genetics/Internal Medicine, Yale University",2,0.01126,0.9112,0.00402,0.18979,0.98137,0.7838,0.32952,0.50602,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-08-10,Pharyngula,Embryo,Trunk,Surface Structure
70970,SRR21007398,SRX17024128,SRS14609021,SRP390913,PRJNA868351,Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [scRNA seq],GSE210941,Transcriptome Analysis,Investigate the role of miR128 in the EHT process and the formation of nHSPCs Overall design: Comparative gene expression  analysis of RNA seq data for WT and MT samples for miRNA128 in Human and Fish,parent bioproject:PRJNA868347,pubmed:37460694,,gRNA csnk1  26HPF  scRNAseq,GSM6443155,,source name:trunk tissue containing the AGM|cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF|geo loc name:missing|collection date:missing,gRNA csnk1  26HPF  scRNAseq,The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: Tab separated values files and matrix files,trunk tissue containing the AGM,,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b g3’UTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF,GSM6443155,GSM6443155: gRNA csnk1  26HPF  scRNAseq; Danio rerio; RNA Seq,GSM6443155 r1,GSM6443155,1,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b gthree primeUTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP390913,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=csnk1a DRT S2 L004 I1 001.fastq.gz   read2PairFiles=csnk1a DRT S2 L004 R1 001.fastq.gz   read3PairFiles=csnk1a DRT S2 L004 R2 001.fastq.gz,csnk1a_DRT_S2_L004_I1_001.fastq.gz csnk1a_DRT_S2_L004_R1_001.fastq.gz csnk1a_DRT_S2_L004_R2_001.fastq.gz,fastq fastq fastq,17642162328.0,138914664.0,GSM6443155 r2,0:8 1:28 2:91,A:4700864535;C:3672134070;G:3805292893;T:4351958835;N:594683,8,28,91,,4700864535,3672134070,3805292893,4351958835,594683,SRX17024128,SRS14609021,SRA1473366,"Nicoli Lab, Genetics/Internal Medicine, Yale University","Nicoli Lab, Genetics/Internal Medicine, Yale University",2,0.01083,0.91228,0.00389,0.19017,0.98175,0.78413,0.34007,0.51895,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-08-10,Pharyngula,Embryo,Trunk,Surface Structure
70971,SRR21007399,SRX17024127,SRS14609020,SRP390913,PRJNA868351,Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [scRNA seq],GSE210941,Transcriptome Analysis,Investigate the role of miR128 in the EHT process and the formation of nHSPCs Overall design: Comparative gene expression  analysis of RNA seq data for WT and MT samples for miRNA128 in Human and Fish,parent bioproject:PRJNA868347,pubmed:37460694,,MT  26HPF  scRNAseq,GSM6443154,,source name:trunk tissue containing the AGM|cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF|geo loc name:missing|collection date:missing,MT  26HPF  scRNAseq,The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: Tab separated values files and matrix files,trunk tissue containing the AGM,,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b g3’UTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF,GSM6443154,GSM6443154: MT  26HPF  scRNAseq; Danio rerio; RNA Seq,GSM6443154 r1,GSM6443154,1,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b gthree primeUTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP390913,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=MT DRT S2 L004 I1 001.fastq.gz   read2PairFiles=MT DRT S2 L004 R1 001.fastq.gz   read3PairFiles=MT DRT S2 L004 R2 001.fastq.gz,MT_DRT_S2_L004_I1_001.fastq.gz MT_DRT_S2_L004_R1_001.fastq.gz MT_DRT_S2_L004_R2_001.fastq.gz,fastq fastq fastq,44640313691.0,351498533.0,GSM6443154 r1,0:8 1:28 2:91,A:11802470987;C:9130307392;G:9708029949;T:11186763112;N:753987,8,28,91,,11802470987,9130307392,9708029949,11186763112,753987,SRX17024127,SRS14609020,SRA1473366,"Nicoli Lab, Genetics/Internal Medicine, Yale University","Nicoli Lab, Genetics/Internal Medicine, Yale University",2,0.01069,0.92492,0.00314,0.17525,0.98338,0.79586,0.42895,0.5135,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-08-10,Pharyngula,Embryo,Trunk,Surface Structure
70972,SRR21007400,SRX17024126,SRS14609019,SRP390913,PRJNA868351,Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [scRNA seq],GSE210941,Transcriptome Analysis,Investigate the role of miR128 in the EHT process and the formation of nHSPCs Overall design: Comparative gene expression  analysis of RNA seq data for WT and MT samples for miRNA128 in Human and Fish,parent bioproject:PRJNA868347,pubmed:37460694,,WT  26HPF  scRNAseq,GSM6443153,,source name:trunk tissue containing the AGM|cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF|geo loc name:missing|collection date:missing,WT  26HPF  scRNAseq,The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: Tab separated values files and matrix files,trunk tissue containing the AGM,,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b g3’UTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF,GSM6443153,GSM6443153: WT  26HPF  scRNAseq; Danio rerio; RNA Seq,GSM6443153 r1,GSM6443153,1,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b gthree primeUTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP390913,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=WT DRT S1 L004 I1 001.fastq.gz   read2PairFiles=WT DRT S1 L004 R1 001.fastq.gz   read3PairFiles=WT DRT S1 L004 R2 001.fastq.gz,WT_DRT_S1_L004_I1_001.fastq.gz WT_DRT_S1_L004_R1_001.fastq.gz WT_DRT_S1_L004_R2_001.fastq.gz,fastq fastq fastq,63333837772.0,498691636.0,GSM6443153 r1,0:8 1:28 2:91,A:16776941902;C:12869180260;G:13716776874;T:15980339022;N:1066626,8,28,91,,16776941902,12869180260,13716776874,15980339022,1066626,SRX17024126,SRS14609019,SRA1473366,"Nicoli Lab, Genetics/Internal Medicine, Yale University","Nicoli Lab, Genetics/Internal Medicine, Yale University",2,0.00896,0.91613,0.0026,0.16276,0.98466,0.79279,0.44896,0.53257,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-08-10,Pharyngula,Embryo,Trunk,Surface Structure
71632,SRR21855290,SRX17843605,SRS15365430,SRP401856,PRJNA889065,A Tessellated Lymphoid Network Provides Whole Body Antigen Surveillance in Zebrafish,GSE215189,Transcriptome Analysis,T cells survey the host for cognate antigen in mammals by trafficking to and searching within lymph nodes distributed throughout the body. Non mammalian jawed vertebrates lack lymph nodes but still maintain highly diverse repertoires of T cells. How these T cells find antigen in hosts devoid of lymph nodes remains wholly unclear. In this study  we exploit the in vivo imaging amenability of the zebrafish to investigate T cell organization  trafficking  and antigen surveillance in an animal completely lacking lymph nodes. We find that T cells organize into a previously undescribed whole body scale associated pattern that we have named the tessellated lymphoid network TLN. We find that the TLN harbors significantly more T cells than the gills  gut  kidney  and spleen  as well as populations of antigen presenting cells  suggesting a central role in adaptive immune responses in fish. Within the TLN  T cells perform a highly directional ballistic streaming mode of motility  allowing them to traffic through the host in a coordinated ventral to dorsal loop. Local infection results in a dramatic shift in T cell motility  from rapid streaming to a slower random walk in regions proximal to the infection. Here  T cells sequentially interact with and ultimately form stable contacts with antigen presenting cells. Finally  T cells within the TLN of infected fish show transcriptional changes consistent with TCR signaling and subsequent T cell activation. The TLN thus provides a mechanism for T cells to both traffic through the host and  in the context of an infection  effectively scan for and detect antigen  mirroring the function of lymph nodes in mammals. Overall design: Adult zebrafish either without xxx or infected by L. monocytogenes through puncture wounding were euthanized and descaled to collect associated cells at 4 days post infection. Libraries were constructed from these cells using the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and sequenced using NovaSeq6000 Illumina with read lengths of 29 bp + 90 bp Read1 + Read2.,,pubmed:37155881,,Infected  scRNAseq,GSM6625507,,tissue:Descaled cells|cell type:Descaled cells|treatment:infected,Infected  scRNAseq,Raw FASTQ files were processed by cellranger 6.1.2 10x Genomics for demultiplexing  barcoded processing  and gene counting. Assembly: zv11 Supplementary files format and content: Tab separated values files and matrix files,Descaled cells,,Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS  Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head  and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal  dorsal  and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension  and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15  penicillin streptomycin  and 2% FBS in a 15 mL falcon tube  washed  resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells  and washed once more with cell isolation media. Library was performed according to the manufacter’s instructions Chromium Single Cell Gene Expression Solution 3’ v2  10x Genomics.,,cell type:Descaled cells|treatment:infected,GSM6625507,GSM6625507: Infected  scRNAseq; Danio rerio; RNA Seq,GSM6625507 r1,GSM6625507,1,Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS  Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head  and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal  dorsal  and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension  and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15  penicillin streptomycin  and 2% FBS in a 15 mL falcon tube  washed  resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells  and washed once more with cell isolation media. Library was performed according to the manufacter's instructions Chromium Single Cell Gene Expression Solution three prime v2  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP401856,,loader:fastq load.py,Infected_S2_L001_R1_001.fastq.gz Infected_S2_L001_R2_001.fastq.gz,fastq fastq,27971148231.0,239069643.0,GSM6625507 r1,0:28 1:89,A:8061885724;C:6040148313;G:6562354866;T:7306186742;N:572586,28,89,,,8061885724,6040148313,6562354866,7306186742,572586,SRX17843605,SRS15365430,SRA1517576,"Ting Wang, Genetics, Washington University St Louis","Anna Huttenlocher, Pediatrics, University of Wisconsin School of Medicine and Public Health",2,0.00829,0.90109,0.0031,0.16974,0.98742,0.79249,0.29098,0.56795,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2022-10-10,Adult,Adult,Scale,Surface Structure
71633,SRR21855291,SRX17843605,SRS15365430,SRP401856,PRJNA889065,A Tessellated Lymphoid Network Provides Whole Body Antigen Surveillance in Zebrafish,GSE215189,Transcriptome Analysis,T cells survey the host for cognate antigen in mammals by trafficking to and searching within lymph nodes distributed throughout the body. Non mammalian jawed vertebrates lack lymph nodes but still maintain highly diverse repertoires of T cells. How these T cells find antigen in hosts devoid of lymph nodes remains wholly unclear. In this study  we exploit the in vivo imaging amenability of the zebrafish to investigate T cell organization  trafficking  and antigen surveillance in an animal completely lacking lymph nodes. We find that T cells organize into a previously undescribed whole body scale associated pattern that we have named the tessellated lymphoid network TLN. We find that the TLN harbors significantly more T cells than the gills  gut  kidney  and spleen  as well as populations of antigen presenting cells  suggesting a central role in adaptive immune responses in fish. Within the TLN  T cells perform a highly directional ballistic streaming mode of motility  allowing them to traffic through the host in a coordinated ventral to dorsal loop. Local infection results in a dramatic shift in T cell motility  from rapid streaming to a slower random walk in regions proximal to the infection. Here  T cells sequentially interact with and ultimately form stable contacts with antigen presenting cells. Finally  T cells within the TLN of infected fish show transcriptional changes consistent with TCR signaling and subsequent T cell activation. The TLN thus provides a mechanism for T cells to both traffic through the host and  in the context of an infection  effectively scan for and detect antigen  mirroring the function of lymph nodes in mammals. Overall design: Adult zebrafish either without xxx or infected by L. monocytogenes through puncture wounding were euthanized and descaled to collect associated cells at 4 days post infection. Libraries were constructed from these cells using the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and sequenced using NovaSeq6000 Illumina with read lengths of 29 bp + 90 bp Read1 + Read2.,,pubmed:37155881,,Infected  scRNAseq,GSM6625507,,tissue:Descaled cells|cell type:Descaled cells|treatment:infected,Infected  scRNAseq,Raw FASTQ files were processed by cellranger 6.1.2 10x Genomics for demultiplexing  barcoded processing  and gene counting. Assembly: zv11 Supplementary files format and content: Tab separated values files and matrix files,Descaled cells,,Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS  Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head  and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal  dorsal  and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension  and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15  penicillin streptomycin  and 2% FBS in a 15 mL falcon tube  washed  resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells  and washed once more with cell isolation media. Library was performed according to the manufacter’s instructions Chromium Single Cell Gene Expression Solution 3’ v2  10x Genomics.,,cell type:Descaled cells|treatment:infected,GSM6625507,GSM6625507: Infected  scRNAseq; Danio rerio; RNA Seq,GSM6625507 r1,GSM6625507,1,Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS  Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head  and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal  dorsal  and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension  and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15  penicillin streptomycin  and 2% FBS in a 15 mL falcon tube  washed  resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells  and washed once more with cell isolation media. Library was performed according to the manufacter's instructions Chromium Single Cell Gene Expression Solution three prime v2  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP401856,,loader:fastq load.py,Infected_S2_L002_R1_001.fastq.gz Infected_S2_L002_R2_001.fastq.gz,fastq fastq,28948392252.0,247422156.0,GSM6625507 r2,0:28 1:89,A:8329225374;C:6258698724;G:6802339342;T:7557690208;N:438604,28,89,,,8329225374,6258698724,6802339342,7557690208,438604,SRX17843605,SRS15365430,SRA1517576,"Ting Wang, Genetics, Washington University St Louis","Anna Huttenlocher, Pediatrics, University of Wisconsin School of Medicine and Public Health",2,0.00815,0.89934,0.00296,0.16878,0.98717,0.79032,0.32081,0.56999,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2022-10-10,Adult,Adult,Scale,Surface Structure
71634,SRR21855292,SRX17843604,SRS15365429,SRP401856,PRJNA889065,A Tessellated Lymphoid Network Provides Whole Body Antigen Surveillance in Zebrafish,GSE215189,Transcriptome Analysis,T cells survey the host for cognate antigen in mammals by trafficking to and searching within lymph nodes distributed throughout the body. Non mammalian jawed vertebrates lack lymph nodes but still maintain highly diverse repertoires of T cells. How these T cells find antigen in hosts devoid of lymph nodes remains wholly unclear. In this study  we exploit the in vivo imaging amenability of the zebrafish to investigate T cell organization  trafficking  and antigen surveillance in an animal completely lacking lymph nodes. We find that T cells organize into a previously undescribed whole body scale associated pattern that we have named the tessellated lymphoid network TLN. We find that the TLN harbors significantly more T cells than the gills  gut  kidney  and spleen  as well as populations of antigen presenting cells  suggesting a central role in adaptive immune responses in fish. Within the TLN  T cells perform a highly directional ballistic streaming mode of motility  allowing them to traffic through the host in a coordinated ventral to dorsal loop. Local infection results in a dramatic shift in T cell motility  from rapid streaming to a slower random walk in regions proximal to the infection. Here  T cells sequentially interact with and ultimately form stable contacts with antigen presenting cells. Finally  T cells within the TLN of infected fish show transcriptional changes consistent with TCR signaling and subsequent T cell activation. The TLN thus provides a mechanism for T cells to both traffic through the host and  in the context of an infection  effectively scan for and detect antigen  mirroring the function of lymph nodes in mammals. Overall design: Adult zebrafish either without xxx or infected by L. monocytogenes through puncture wounding were euthanized and descaled to collect associated cells at 4 days post infection. Libraries were constructed from these cells using the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and sequenced using NovaSeq6000 Illumina with read lengths of 29 bp + 90 bp Read1 + Read2.,,pubmed:37155881,,Control  scRNAseq,GSM6625506,,tissue:Descaled cells|cell type:Descaled cells|treatment:control,Control  scRNAseq,Raw FASTQ files were processed by cellranger 6.1.2 10x Genomics for demultiplexing  barcoded processing  and gene counting. Assembly: zv11 Supplementary files format and content: Tab separated values files and matrix files,Descaled cells,,Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS  Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head  and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal  dorsal  and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension  and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15  penicillin streptomycin  and 2% FBS in a 15 mL falcon tube  washed  resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells  and washed once more with cell isolation media. Library was performed according to the manufacter’s instructions Chromium Single Cell Gene Expression Solution 3’ v2  10x Genomics.,,cell type:Descaled cells|treatment:control,GSM6625506,GSM6625506: Control  scRNAseq; Danio rerio; RNA Seq,GSM6625506 r1,GSM6625506,1,Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS  Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head  and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal  dorsal  and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension  and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15  penicillin streptomycin  and 2% FBS in a 15 mL falcon tube  washed  resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells  and washed once more with cell isolation media. Library was performed according to the manufacter's instructions Chromium Single Cell Gene Expression Solution three prime v2  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP401856,,loader:fastq load.py,Control_S1_L001_R1_001.fastq.gz Control_S1_L001_R2_001.fastq.gz,fastq fastq,22227506496.0,189978688.0,GSM6625506 r1,0:28 1:89,A:6692049340;C:4739918301;G:5329051962;T:5466033150;N:453743,28,89,,,6692049340,4739918301,5329051962,5466033150,453743,SRX17843604,SRS15365429,SRA1517576,"Ting Wang, Genetics, Washington University St Louis","Anna Huttenlocher, Pediatrics, University of Wisconsin School of Medicine and Public Health",2,0.01277,0.88905,0.00634,0.17657,0.98879,0.78119,0.33278,0.56433,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2022-10-10,Adult,Adult,Scale,Surface Structure
71635,SRR21855293,SRX17843604,SRS15365429,SRP401856,PRJNA889065,A Tessellated Lymphoid Network Provides Whole Body Antigen Surveillance in Zebrafish,GSE215189,Transcriptome Analysis,T cells survey the host for cognate antigen in mammals by trafficking to and searching within lymph nodes distributed throughout the body. Non mammalian jawed vertebrates lack lymph nodes but still maintain highly diverse repertoires of T cells. How these T cells find antigen in hosts devoid of lymph nodes remains wholly unclear. In this study  we exploit the in vivo imaging amenability of the zebrafish to investigate T cell organization  trafficking  and antigen surveillance in an animal completely lacking lymph nodes. We find that T cells organize into a previously undescribed whole body scale associated pattern that we have named the tessellated lymphoid network TLN. We find that the TLN harbors significantly more T cells than the gills  gut  kidney  and spleen  as well as populations of antigen presenting cells  suggesting a central role in adaptive immune responses in fish. Within the TLN  T cells perform a highly directional ballistic streaming mode of motility  allowing them to traffic through the host in a coordinated ventral to dorsal loop. Local infection results in a dramatic shift in T cell motility  from rapid streaming to a slower random walk in regions proximal to the infection. Here  T cells sequentially interact with and ultimately form stable contacts with antigen presenting cells. Finally  T cells within the TLN of infected fish show transcriptional changes consistent with TCR signaling and subsequent T cell activation. The TLN thus provides a mechanism for T cells to both traffic through the host and  in the context of an infection  effectively scan for and detect antigen  mirroring the function of lymph nodes in mammals. Overall design: Adult zebrafish either without xxx or infected by L. monocytogenes through puncture wounding were euthanized and descaled to collect associated cells at 4 days post infection. Libraries were constructed from these cells using the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and sequenced using NovaSeq6000 Illumina with read lengths of 29 bp + 90 bp Read1 + Read2.,,pubmed:37155881,,Control  scRNAseq,GSM6625506,,tissue:Descaled cells|cell type:Descaled cells|treatment:control,Control  scRNAseq,Raw FASTQ files were processed by cellranger 6.1.2 10x Genomics for demultiplexing  barcoded processing  and gene counting. Assembly: zv11 Supplementary files format and content: Tab separated values files and matrix files,Descaled cells,,Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS  Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head  and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal  dorsal  and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension  and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15  penicillin streptomycin  and 2% FBS in a 15 mL falcon tube  washed  resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells  and washed once more with cell isolation media. Library was performed according to the manufacter’s instructions Chromium Single Cell Gene Expression Solution 3’ v2  10x Genomics.,,cell type:Descaled cells|treatment:control,GSM6625506,GSM6625506: Control  scRNAseq; Danio rerio; RNA Seq,GSM6625506 r1,GSM6625506,1,Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS  Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head  and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal  dorsal  and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension  and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15  penicillin streptomycin  and 2% FBS in a 15 mL falcon tube  washed  resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells  and washed once more with cell isolation media. Library was performed according to the manufacter's instructions Chromium Single Cell Gene Expression Solution three prime v2  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP401856,,loader:fastq load.py,Control_S1_L002_R1_001.fastq.gz Control_S1_L002_R2_001.fastq.gz,fastq fastq,22948305003.0,196139359.0,GSM6625506 r2,0:28 1:89,A:6891536928;C:4902194962;G:5508766043;T:5645479908;N:327162,28,89,,,6891536928,4902194962,5508766043,5645479908,327162,SRX17843604,SRS15365429,SRA1517576,"Ting Wang, Genetics, Washington University St Louis","Anna Huttenlocher, Pediatrics, University of Wisconsin School of Medicine and Public Health",2,0.01284,0.88937,0.00623,0.17647,0.98926,0.78315,0.32038,0.56842,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2022-10-10,Adult,Adult,Scale,Surface Structure
71755,SRR22013536,SRX17995702,SRS15506856,SRP404046,PRJNA893216,Insulin like growth factor receptor / mTOR signaling elevates global translation to accelerate zebrafish fin regenerative outgrowth,GSE216359,Transcriptome Analysis,We generate a single cell transcriptome dataset to characterize zebrafish fin regenerative outgrowth and explore coordinated cell behaviors. Overall design: Regenerated fin tissue was collected from 3 and 7 dy post amputation zebrafish caudal fins and analyzed using scRNA seq,,pubmed:37290497,,7 dpa  scRNA seq,GSM6670935,,source name:Caudal fin|tissue:Caudal fin|time:7 dpa|genotype:Tgsp7:EGFP;Tgtph1b:mCherry|Stage:Adult|geo loc name:missing|collection date:missing,7 dpa  scRNA seq,Pseudoalignment and processing of raw reads was done in Kallisto/Bustools https://github.com/pachterlab/kb python to generate a cell data set for Monocle3 https://cole trapnell lab.github.io/monocle3/ Assembly: GRCz11.99 Supplementary files format and content: rds file of cell data set,Caudal fin,,Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice  diced  then washed with L 15 media supplemented with 1X GlutaMax  1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml  Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 μm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. Library was performed according to the manufacturer’s instructions single cell 3’ v3 protocol  10x Genomics. Briefly  cells from fin tissue were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up  amplified by PCR  and the appropiate sized fragments were selected for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Caudal fin|time:7 dpa|genotype:Tgsp7:EGFP;Tgtph1b:mCherry|Stage:Adult,GSM6670935,GSM6670935: 7 dpa  scRNA seq; Danio rerio; RNA Seq,GSM6670935 r1,GSM6670935,1,Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice  diced  then washed with L 15 media supplemented with 1X GlutaMax  1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml  Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 μm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. Library was performed according to the manufacturer's instructions single cell three prime v3 protocol  10x Genomics. Briefly  cells from fin tissue were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up  amplified by PCR  and the appropiate sized fragments were selected for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP404046,,loader:fastq load.py,3668_7dpa_S2_L001_I1_001.fastq.gz 3668_7dpa_S2_L001_R1_001.fastq.gz 3668_7dpa_S2_L001_R2_001.fastq.gz,fastq fastq fastq,14309041035.0,104445555.0,GSM6670935 r1,0:8 1:28 2:101,A:3095734143;C:2218234178;G:2235474863;T:2997266454;N:2291417,8,28,101,,3095734143,2218234178,2235474863,2997266454,2291417,SRX17995702,SRS15506856,SRA1525679,"Stankunas, Institute of Molecular Biology, University of Oregon","Stankunas, Institute of Molecular Biology, University of Oregon",1,0.89077,,0.20943,,0.79935,,0.6085,,101,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2022-10-22,Adult,Adult,Fin,Surface Structure
71756,SRR22013537,SRX17995702,SRS15506856,SRP404046,PRJNA893216,Insulin like growth factor receptor / mTOR signaling elevates global translation to accelerate zebrafish fin regenerative outgrowth,GSE216359,Transcriptome Analysis,We generate a single cell transcriptome dataset to characterize zebrafish fin regenerative outgrowth and explore coordinated cell behaviors. Overall design: Regenerated fin tissue was collected from 3 and 7 dy post amputation zebrafish caudal fins and analyzed using scRNA seq,,pubmed:37290497,,7 dpa  scRNA seq,GSM6670935,,source name:Caudal fin|tissue:Caudal fin|time:7 dpa|genotype:Tgsp7:EGFP;Tgtph1b:mCherry|Stage:Adult|geo loc name:missing|collection date:missing,7 dpa  scRNA seq,Pseudoalignment and processing of raw reads was done in Kallisto/Bustools https://github.com/pachterlab/kb python to generate a cell data set for Monocle3 https://cole trapnell lab.github.io/monocle3/ Assembly: GRCz11.99 Supplementary files format and content: rds file of cell data set,Caudal fin,,Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice  diced  then washed with L 15 media supplemented with 1X GlutaMax  1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml  Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 μm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. Library was performed according to the manufacturer’s instructions single cell 3’ v3 protocol  10x Genomics. Briefly  cells from fin tissue were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up  amplified by PCR  and the appropiate sized fragments were selected for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Caudal fin|time:7 dpa|genotype:Tgsp7:EGFP;Tgtph1b:mCherry|Stage:Adult,GSM6670935,GSM6670935: 7 dpa  scRNA seq; Danio rerio; RNA Seq,GSM6670935 r1,GSM6670935,1,Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice  diced  then washed with L 15 media supplemented with 1X GlutaMax  1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml  Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 μm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. Library was performed according to the manufacturer's instructions single cell three prime v3 protocol  10x Genomics. Briefly  cells from fin tissue were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up  amplified by PCR  and the appropiate sized fragments were selected for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP404046,,loader:fastq load.py,3669_7dpa_S5_L002_I1_001.fastq.gz 3669_7dpa_S5_L002_R1_001.fastq.gz 3669_7dpa_S5_L002_R2_001.fastq.gz,fastq fastq fastq,14699346911.0,107294503.0,GSM6670935 r2,0:8 1:28 2:101,A:3181472399;C:2279044984;G:2296050130;T:3077615290;N:2562000,8,28,101,,3181472399,2279044984,2296050130,3077615290,2562000,SRX17995702,SRS15506856,SRA1525679,"Stankunas, Institute of Molecular Biology, University of Oregon","Stankunas, Institute of Molecular Biology, University of Oregon",1,0.89055,,0.21159,,0.80168,,0.60887,,101,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2022-10-22,Adult,Adult,Fin,Surface Structure
71757,SRR22013538,SRX17995701,SRS15506855,SRP404046,PRJNA893216,Insulin like growth factor receptor / mTOR signaling elevates global translation to accelerate zebrafish fin regenerative outgrowth,GSE216359,Transcriptome Analysis,We generate a single cell transcriptome dataset to characterize zebrafish fin regenerative outgrowth and explore coordinated cell behaviors. Overall design: Regenerated fin tissue was collected from 3 and 7 dy post amputation zebrafish caudal fins and analyzed using scRNA seq,,pubmed:37290497,,3 dpa  scRNA seq,GSM6670934,,source name:Caudal fin|tissue:Caudal fin|time:3 dpa|genotype:Tgsp7:EGFP;Tgtph1b:mCherry|Stage:Adult|geo loc name:missing|collection date:missing,3 dpa  scRNA seq,Pseudoalignment and processing of raw reads was done in Kallisto/Bustools https://github.com/pachterlab/kb python to generate a cell data set for Monocle3 https://cole trapnell lab.github.io/monocle3/ Assembly: GRCz11.99 Supplementary files format and content: rds file of cell data set,Caudal fin,,Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice  diced  then washed with L 15 media supplemented with 1X GlutaMax  1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml  Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 μm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. Library was performed according to the manufacturer’s instructions single cell 3’ v3 protocol  10x Genomics. Briefly  cells from fin tissue were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up  amplified by PCR  and the appropiate sized fragments were selected for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Caudal fin|time:3 dpa|genotype:Tgsp7:EGFP;Tgtph1b:mCherry|Stage:Adult,GSM6670934,GSM6670934: 3 dpa  scRNA seq; Danio rerio; RNA Seq,GSM6670934 r1,GSM6670934,1,Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice  diced  then washed with L 15 media supplemented with 1X GlutaMax  1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml  Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 μm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. Library was performed according to the manufacturer',,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP404046,,loader:fastq load.py,3668_3dpa_S1_L001_I1_001.fastq.gz 3668_3dpa_S1_L001_R1_001.fastq.gz 3668_3dpa_S1_L001_R2_001.fastq.gz,fastq fastq fastq,18445973865.0,134642145.0,GSM6670934 r1,0:8 1:28 2:101,A:4016744063;C:2790570873;G:2912735479;T:3875859487;N:2946743,8,28,101,,4016744063,2790570873,2912735479,3875859487,2946743,SRX17995701,SRS15506855,SRA1525679,"Stankunas, Institute of Molecular Biology, University of Oregon","Stankunas, Institute of Molecular Biology, University of Oregon",1,0.92077,,0.19536,,0.78597,,0.5661,,101,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2022-10-22,Adult,Adult,Fin,Surface Structure
71758,SRR22013539,SRX17995701,SRS15506855,SRP404046,PRJNA893216,Insulin like growth factor receptor / mTOR signaling elevates global translation to accelerate zebrafish fin regenerative outgrowth,GSE216359,Transcriptome Analysis,We generate a single cell transcriptome dataset to characterize zebrafish fin regenerative outgrowth and explore coordinated cell behaviors. Overall design: Regenerated fin tissue was collected from 3 and 7 dy post amputation zebrafish caudal fins and analyzed using scRNA seq,,pubmed:37290497,,3 dpa  scRNA seq,GSM6670934,,source name:Caudal fin|tissue:Caudal fin|time:3 dpa|genotype:Tgsp7:EGFP;Tgtph1b:mCherry|Stage:Adult|geo loc name:missing|collection date:missing,3 dpa  scRNA seq,Pseudoalignment and processing of raw reads was done in Kallisto/Bustools https://github.com/pachterlab/kb python to generate a cell data set for Monocle3 https://cole trapnell lab.github.io/monocle3/ Assembly: GRCz11.99 Supplementary files format and content: rds file of cell data set,Caudal fin,,Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice  diced  then washed with L 15 media supplemented with 1X GlutaMax  1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml  Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 μm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. Library was performed according to the manufacturer’s instructions single cell 3’ v3 protocol  10x Genomics. Briefly  cells from fin tissue were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up  amplified by PCR  and the appropiate sized fragments were selected for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Caudal fin|time:3 dpa|genotype:Tgsp7:EGFP;Tgtph1b:mCherry|Stage:Adult,GSM6670934,GSM6670934: 3 dpa  scRNA seq; Danio rerio; RNA Seq,GSM6670934 r1,GSM6670934,1,Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice  diced  then washed with L 15 media supplemented with 1X GlutaMax  1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml  Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 μm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. Library was performed according to the manufacturer',,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP404046,,loader:fastq load.py,3669_3dpa_S4_L002_I1_001.fastq.gz 3669_3dpa_S4_L002_R1_001.fastq.gz 3669_3dpa_S4_L002_R2_001.fastq.gz,fastq fastq fastq,18947450035.0,138302555.0,GSM6670934 r2,0:8 1:28 2:101,A:4126083375;C:2867407006;G:2991995583;T:3979778947;N:3293144,8,28,101,,4126083375,2867407006,2991995583,3979778947,3293144,SRX17995701,SRS15506855,SRA1525679,"Stankunas, Institute of Molecular Biology, University of Oregon","Stankunas, Institute of Molecular Biology, University of Oregon",1,0.91921,,0.19517,,0.78524,,0.57129,,101,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2022-10-22,Adult,Adult,Fin,Surface Structure
73980,SRR23292532,SRX19235642,SRS16640049,SRP420343,PRJNA930044,scRNAseq gene expression profile of zebrafish jaw joint cells post IOM ligament transection.,GSE224197,Transcriptome Analysis,Adult zebrafish have the capacity to regenerate craniofacial ligament tissue following a complete transection injury. How this robust skeletal regeneration is achieved remains undefined. Here  we use single cell RNA sequencing to profile RNA expression from FACS sorted cranial neural crest lineage and non cranial neural crest lineage cells including skin and immune populations in the first 3 days post ligament injury. Overall design: To understand the cellular contributors and molecular regulation of craniofacial ligament regeneration in adult zebrafish  we collected jaw joint cells for single cell RNA sequencing following ligament injury. post IOM ligament transection injury and in uninjured and SHAM surgical controls  neural crest lineage cells DsRed and non neural crest lineage cells BFP were isolated using Fluorescence activated cell sorting FACS from jaw joints microdissected from Sox10:Cre;actb2:loxP BFP STOP loxP DsRed transgenic fish and analyzed using scRNAseq.,,pubmed:37726321,,Sox10Cre BtR IOM 3dplt Red  scRNAseq,GSM7017325,,source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:CNCC enriched|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection,Sox10Cre BtR IOM 3dplt Red  scRNAseq,Fastq files were aligned to GRCz11 using CellRanger v3.0.0 from 10X Genomics. Assembly: GRCz11.fa Supplementary files format and content: Processed data for each sample includes CellRanger outputs: barcode  features  and matrix files in tsv format.,jaw joint,IOM transection surgery was performed on adult zebrafish and collected at 1 and 3 xxx post injury for 24hplt and 3dplt samples. Controls include uninjured samples and SHAM injury samples. For SHAM  fish were anaesthetized as per experimental samples but only the skin overlying the IOM ligament was lightly nicked. Joints were collected 1 and 3 days post surgery for 24hSHAM and 3dSHAM samples.,Microdissected joints were mechanically and enzymatically dissociated prior to FACS sorting with either enrichment for DsRed+ cranial neural crest CNCC lineage cells or no enrichment in BFP+ libraries. FACS sorted cells were processed using the 10X Chromium controller for single cell profiling. Barcoded single cell cDNA library constuction performed as per manufacturer's instructions using the 10X scRNAseq Kit v2.,,tissue:jaw joint|age:3 5mpf adult|cell type:CNCC enriched|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection,GSM7017325,GSM7017325: Sox10Cre BtR IOM 3dplt Red  scRNAseq; Danio rerio; RNA Seq,GSM7017325 r1,GSM7017325,1,Microdissected joints were mechanically and enzymatically dissociated prior to FACS sorting with either enrichment for DsRed+ cranial neural crest CNCC lineage cells or no enrichment in BFP+ libraries. FACS sorted cells were processed using the 10X Chromium controller for single cell profiling. Barcoded single cell cDNA library constuction performed as per manufacturer's instructions using the 10X scRNAseq Kit v2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP420343,,,Sox10Cre_BtR_IOM_3dplt_DsRed-1_S33_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_3dplt_DsRed-1_S33_L001_R2_001.fastq.gz,fastq fastq,3212586883.0,21782952.0,GSM7017325 r1,0:27 1:120.48,A:889247747;C:712836063;G:736196241;T:871677201;N:2629631,27,120,,,889247747,712836063,736196241,871677201,2629631,SRX19235642,SRS16640049,SRA1583003,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",2,0.00151,0.92087,0.0007,0.13437,0.99748,0.87065,0.41025,0.52913,27,121,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-01-31,Adult,Adult,Jaw,Surface Structure
73981,SRR23292533,SRX19235642,SRS16640049,SRP420343,PRJNA930044,scRNAseq gene expression profile of zebrafish jaw joint cells post IOM ligament transection.,GSE224197,Transcriptome Analysis,Adult zebrafish have the capacity to regenerate craniofacial ligament tissue following a complete transection injury. How this robust skeletal regeneration is achieved remains undefined. Here  we use single cell RNA sequencing to profile RNA expression from FACS sorted cranial neural crest lineage and non cranial neural crest lineage cells including skin and immune populations in the first 3 days post ligament injury. Overall design: To understand the cellular contributors and molecular regulation of craniofacial ligament regeneration in adult zebrafish  we collected jaw joint cells for single cell RNA sequencing following ligament injury. post IOM ligament transection injury and in uninjured and SHAM surgical controls  neural crest lineage cells DsRed and non neural crest lineage cells BFP were isolated using Fluorescence activated cell sorting FACS from jaw joints microdissected from Sox10:Cre;actb2:loxP BFP STOP loxP DsRed transgenic fish and analyzed using scRNAseq.,,pubmed:37726321,,Sox10Cre BtR IOM 3dplt Red  scRNAseq,GSM7017325,,source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:CNCC enriched|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection,Sox10Cre BtR IOM 3dplt Red  scRNAseq,Fastq files were aligned to GRCz11 using CellRanger v3.0.0 from 10X Genomics. Assembly: GRCz11.fa Supplementary files format and content: Processed data for each sample includes CellRanger outputs: barcode  features  and matrix files in tsv format.,jaw joint,IOM transection surgery was performed on adult zebrafish and collected at 1 and 3 xxx post injury for 24hplt and 3dplt samples. Controls include uninjured samples and SHAM injury samples. For SHAM  fish were anaesthetized as per experimental samples but only the skin overlying the IOM ligament was lightly nicked. Joints were collected 1 and 3 days post surgery for 24hSHAM and 3dSHAM samples.,Microdissected joints were mechanically and enzymatically dissociated prior to FACS sorting with either enrichment for DsRed+ cranial neural crest CNCC lineage cells or no enrichment in BFP+ libraries. FACS sorted cells were processed using the 10X Chromium controller for single cell profiling. Barcoded single cell cDNA library constuction performed as per manufacturer's instructions using the 10X scRNAseq Kit v2.,,tissue:jaw joint|age:3 5mpf adult|cell type:CNCC enriched|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection,GSM7017325,GSM7017325: Sox10Cre BtR IOM 3dplt Red  scRNAseq; Danio rerio; RNA Seq,GSM7017325 r1,GSM7017325,1,Microdissected joints were mechanically and enzymatically dissociated prior to FACS sorting with either enrichment for DsRed+ cranial neural crest CNCC lineage cells or no enrichment in BFP+ libraries. FACS sorted cells were processed using the 10X Chromium controller for single cell profiling. Barcoded single cell cDNA library constuction performed as per manufacturer's instructions using the 10X scRNAseq Kit v2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP420343,,,Sox10Cre_BtR_IOM_3dplt_DsRed-2_S34_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_3dplt_DsRed-2_S34_L001_R2_001.fastq.gz,fastq fastq,3137844278.0,21279993.0,GSM7017325 r2,0:27 1:120.46,A:870482223;C:695563498;G:723319796;T:845918600;N:2560161,27,120,,,870482223,695563498,723319796,845918600,2560161,SRX19235642,SRS16640049,SRA1583003,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",2,0.00159,0.92488,0.00061,0.12748,0.99695,0.85307,0.45077,0.49755,27,118,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-01-31,Adult,Adult,Jaw,Surface Structure
73982,SRR23292534,SRX19235642,SRS16640049,SRP420343,PRJNA930044,scRNAseq gene expression profile of zebrafish jaw joint cells post IOM ligament transection.,GSE224197,Transcriptome Analysis,Adult zebrafish have the capacity to regenerate craniofacial ligament tissue following a complete transection injury. How this robust skeletal regeneration is achieved remains undefined. Here  we use single cell RNA sequencing to profile RNA expression from FACS sorted cranial neural crest lineage and non cranial neural crest lineage cells including skin and immune populations in the first 3 days post ligament injury. Overall design: To understand the cellular contributors and molecular regulation of craniofacial ligament regeneration in adult zebrafish  we collected jaw joint cells for single cell RNA sequencing following ligament injury. post IOM ligament transection injury and in uninjured and SHAM surgical controls  neural crest lineage cells DsRed and non neural crest lineage cells BFP were isolated using Fluorescence activated cell sorting FACS from jaw joints microdissected from Sox10:Cre;actb2:loxP BFP STOP loxP DsRed transgenic fish and analyzed using scRNAseq.,,pubmed:37726321,,Sox10Cre BtR IOM 3dplt Red  scRNAseq,GSM7017325,,source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:CNCC enriched|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection,Sox10Cre BtR IOM 3dplt Red  scRNAseq,Fastq files were aligned to GRCz11 using CellRanger v3.0.0 from 10X Genomics. Assembly: GRCz11.fa Supplementary files format and content: Processed data for each sample includes CellRanger outputs: barcode  features  and matrix files in tsv format.,jaw joint,IOM transection surgery was performed on adult zebrafish and collected at 1 and 3 xxx post injury for 24hplt and 3dplt samples. Controls include uninjured samples and SHAM injury samples. For SHAM  fish were anaesthetized as per experimental samples but only the skin overlying the IOM ligament was lightly nicked. Joints were collected 1 and 3 days post surgery for 24hSHAM and 3dSHAM samples.,Microdissected joints were mechanically and enzymatically dissociated prior to FACS sorting with either enrichment for DsRed+ cranial neural crest CNCC lineage cells or no enrichment in BFP+ libraries. FACS sorted cells were processed using the 10X Chromium controller for single cell profiling. Barcoded single cell cDNA library constuction performed as per manufacturer's instructions using the 10X scRNAseq Kit v2.,,tissue:jaw joint|age:3 5mpf adult|cell type:CNCC enriched|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection,GSM7017325,GSM7017325: Sox10Cre BtR IOM 3dplt Red  scRNAseq; Danio rerio; RNA Seq,GSM7017325 r1,GSM7017325,1,Microdissected joints were mechanically and enzymatically dissociated prior to FACS sorting with either enrichment for DsRed+ cranial neural crest CNCC lineage cells or no enrichment in BFP+ libraries. FACS sorted cells were processed using the 10X Chromium controller for single cell profiling. Barcoded single cell cDNA library constuction performed as per manufacturer's instructions using the 10X scRNAseq Kit v2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP420343,,,Sox10Cre_BtR_IOM_3dplt_DsRed-3_S35_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_3dplt_DsRed-3_S35_L001_R2_001.fastq.gz,fastq fastq,4071005433.0,27610532.0,GSM7017325 r3,0:27 1:120.44,A:1139555452;C:904968992;G:940567540;T:1082637805;N:3275644,27,120,,,1139555452,904968992,940567540,1082637805,3275644,SRX19235642,SRS16640049,SRA1583003,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",2,0.0015,0.92439,0.00071,0.12885,0.9976,0.8617,0.46451,0.53839,27,121,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-01-31,Adult,Adult,Jaw,Surface Structure