{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where technology = \"10x\" and tissue_curation = \"Lateral Line\"", "rows": [[32366, "SRR29152187", "SRX24673329", "SRS21408057", "SRP509548", "PRJNA1115803", "Stem and progenitor cell proliferation are independently regulated by cell type specific cyclinD genes", "GSE268255", "Transcriptome Analysis", "Regeneration and homeostatic turnover of solid tissues depend on the proliferation of symmetrically dividing adult stem cells  which either remain stem cells or differentiate based on their niche position. Here we demonstrate that in zebrafish lateral line sensory organs  stem and progenitor cell proliferation are independently regulated by two cyclinD genes. Loss of ccnd2a impairs stem cell proliferation during development  while loss of ccndx disrupts hair cell progenitor proliferation but allows normal differentiation. Notably  ccnd2a can functionally replace ccndx  indicating that the respective effects of these Cyclins on proliferation are due to cell type specific expression. However  even though hair cell progenitors differentiate normally in ccndx mutants  they are mispolarized due to hes2 and Emx2 downregulation. Thus  regulated proliferation ensures that equal numbers of hair cells are polarized in opposite directions. Our study reveals cell type specific roles for cyclinD genes in regulating the different populations of symmetrically dividing cells governing organ development and regeneration  with implications for regenerative medicine and disease. Overall design: Two replicates per sibling or ccndx mutant were used", null, null, null, "ccndx sibling2", "GSM8288756", null, "tissue:5dpf zebrafish FACS sorted lateral line cells|cell type:Homostasis|genotype:Wildtype|geo loc name:missing|collection date:missing", "ccndx sibling2", "Raw sequencing data were processed using 10X Genomics Cell Ranger pipeline. Reads were demultiplexed into Fastq file format using cellranger mkfastq. Genome index was built by cellranger mkref using zebrafish genome danRer11  ensembl 98 gene model. Data were aligned by STAR aligner and cell counts tables were generated using cellranger count function with default parameters. Assembly: danRer11 Supplementary files format and content: single cell  count matrix in hdf5 format  raw data in bam format.", "5dpf zebrafish FACS sorted lateral line cells", "All cells were collected during homeostasis  no treatments were performed.", "5 dpf zebrafish were anesthetized with Tricane then split between two 70mm cell strainers Falcon and placed in 0.25% Trypsin EDTA Gibco on ice. The larvae from each strainer are then added to a 5ml round bottom tube Falcon and the tissue is broken up via slowly pipetting up and down using a pipette man and a glass pipette VWR keeping the tubes on ice. The total time from placing larvae in trypsin to finishing pipetting is approximately 8 minutes. The tissue is then filtered through 70mm filter BD Biosciences  pelleted for 5 min at 2000rpm at 4oC and then the pellet is resuspended in 1xDPBS/0.04%BSA. The pelleting and resuspension in 1xDPBS/0.04%BSA is repeated two more times. post the final pellet the cells are resuspended in 0.5mL 1xDPBS/0.04%BSA then cells are combined and put through another 70mm filter into a 5ml round bottom tube. Cells are then incubated in Draq5 1/200 dilution for 5 minutes on ice. Draq5+/mCherry+ cells were sorted by the Stowers Institute Cytometry Core Facility using a BD Influx Cell Sorter BD Biosciences  San Jose  CA. USA  with cells collected in tubes containing 10mL 1XDPBS/0.04% BSA. Cells were not fixed in methanol as in previous protocols as we found this gave inconsistent results with 10X Genomics version 3 kits. Sorted cells are then spun down at 350rcf at 4oC for 2 min in a swinging bucket centrifuge with slow deceleration. Most of the supernatant is removed and the cells are resuspended in approximately remaining 100mL. Cells deemed to be at least 80% viable were loaded based on live cell concentration onto a Chromium X Series instrument 10x Genomics and libraries prepared using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 10x Genomics according to manufacturer\u2019s directions. Resulting cDNA and short fragment libraries were checked for quality and quantity using a 2100 Bioanalyzer Agilent Technologies and Qubit Fluorometer Thermo Fisher Scientific. With cells captured estimated at 6 800 9 600 cells per sample  libraries were pooled and sequenced to a depth necessary to achieve at least 30 000 mean reads per cell on an Illumina NextSeq 2000 instrument utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths: 28*10*10*90bp. scRNA seq 10x Genomics", "5dpf zebrafish FACS sorted lateral line cells were used. Standard growing condition were used.", "cell type:Homostasis|genotype:Wildtype", "GSM8288756", "GSM8288756: ccndx sibling2; Danio rerio; RNA Seq", "GSM8288756 r1", "GSM8288756", "1", "5 dpf zebrafish were anesthetized with Tricane then split between two 70mm cell strainers Falcon and placed in 0.25% Trypsin EDTA Gibco on ice. The larvae from each strainer are then added to a 5ml round bottom tube Falcon and the tissue is broken up via slowly pipetting up and down using a pipette man and a glass pipette VWR keeping the tubes on ice. The total time from placing larvae in trypsin to finishing pipetting is approximately 8 minutes. The tissue is then filtered through 70mm filter BD Biosciences  pelleted for 5 min at 2000rpm at 4oC and then the pellet is resuspended in 1xDPBS/0.04%BSA. The pelleting and resuspension in 1xDPBS/0.04%BSA is repeated two more times. post the final pellet the cells are resuspended in 0.5mL 1xDPBS/0.04%BSA then cells are combined and put through another 70mm filter into a 5ml round bottom tube. Cells are then incubated in Draq5 1/200 dilution for 5 minutes on ice. Draq5+/mCherry+ cells were sorted by the Stowers Institute Cytometry Core Facility using a BD Influx Cell Sorter BD Biosciences  San Jose  CA. USA  with cells collected in tubes containing 10mL 1XDPBS/0.04% BSA. Cells were not fixed in methanol as in previous protocols as we found this gave inconsistent results with 10X Genomics version 3 kits. Sorted cells are then spun down at 350rcf at 4oC for 2 min in a swinging bucket centrifuge with slow deceleration. Most of the supernatant is removed and the cells are resuspended in approximately remaining 100mL. Cells deemed to be at least 80% viable were loaded based on live cell concentration onto a Chromium X Series instrument 10x Genomics and libraries prepared using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 10x Genomics according to manufacturer's directions. Resulting cDNA and short fragment libraries were checked for quality and quantity using a 2100 Bioanalyzer Agilent Technologies and Qubit Fluorometer Thermo Fisher Scientific. With cells captured estimated at 6 800 9 600 cells per sample  libraries were pooled and sequenced to a depth necessary to achieve at least 30 000 mean reads per cell on an Illumina NextSeq 2000 instrument utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths: 28*10*10*90bp. scRNA seq 10x Genomics", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP509548", null, "assembly:danRer11|intentional duplicate", "ccndx_sibling2.bam", "10X Genomics bam file", 27438063300.0, 304867370.0, "GSM8288756 r1", "0:90", "A:7768441003;C:5988780076;G:6567352571;T:7111630965;N:1858685", 90, null, null, null, 7768441003, 5988780076, 6567352571, 7111630965, 1858685, "SRX24673329", "SRS21408057", "SRA1876130", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", 1, 0.94768, null, 0.20814, null, 0.75452, null, 0.52756, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-05-23", "Larval", "Larval", "Lateral Line", "Sensory System"], [32367, "SRR29152188", "SRX24673328", "SRS21408056", "SRP509548", "PRJNA1115803", "Stem and progenitor cell proliferation are independently regulated by cell type specific cyclinD genes", "GSE268255", "Transcriptome Analysis", "Regeneration and homeostatic turnover of solid tissues depend on the proliferation of symmetrically dividing adult stem cells  which either remain stem cells or differentiate based on their niche position. Here we demonstrate that in zebrafish lateral line sensory organs  stem and progenitor cell proliferation are independently regulated by two cyclinD genes. Loss of ccnd2a impairs stem cell proliferation during development  while loss of ccndx disrupts hair cell progenitor proliferation but allows normal differentiation. Notably  ccnd2a can functionally replace ccndx  indicating that the respective effects of these Cyclins on proliferation are due to cell type specific expression. However  even though hair cell progenitors differentiate normally in ccndx mutants  they are mispolarized due to hes2 and Emx2 downregulation. Thus  regulated proliferation ensures that equal numbers of hair cells are polarized in opposite directions. Our study reveals cell type specific roles for cyclinD genes in regulating the different populations of symmetrically dividing cells governing organ development and regeneration  with implications for regenerative medicine and disease. Overall design: Two replicates per sibling or ccndx mutant were used", null, null, null, "ccndx sibling1", "GSM8288755", null, "tissue:5dpf zebrafish FACS sorted lateral line cells|cell type:Homostasis|genotype:Wildtype|geo loc name:missing|collection date:missing", "ccndx sibling1", "Raw sequencing data were processed using 10X Genomics Cell Ranger pipeline. Reads were demultiplexed into Fastq file format using cellranger mkfastq. Genome index was built by cellranger mkref using zebrafish genome danRer11  ensembl 98 gene model. Data were aligned by STAR aligner and cell counts tables were generated using cellranger count function with default parameters. Assembly: danRer11 Supplementary files format and content: single cell  count matrix in hdf5 format  raw data in bam format.", "5dpf zebrafish FACS sorted lateral line cells", "All cells were collected during homeostasis  no treatments were performed.", "5 dpf zebrafish were anesthetized with Tricane then split between two 70mm cell strainers Falcon and placed in 0.25% Trypsin EDTA Gibco on ice. The larvae from each strainer are then added to a 5ml round bottom tube Falcon and the tissue is broken up via slowly pipetting up and down using a pipette man and a glass pipette VWR keeping the tubes on ice. The total time from placing larvae in trypsin to finishing pipetting is approximately 8 minutes. The tissue is then filtered through 70mm filter BD Biosciences  pelleted for 5 min at 2000rpm at 4oC and then the pellet is resuspended in 1xDPBS/0.04%BSA. The pelleting and resuspension in 1xDPBS/0.04%BSA is repeated two more times. post the final pellet the cells are resuspended in 0.5mL 1xDPBS/0.04%BSA then cells are combined and put through another 70mm filter into a 5ml round bottom tube. Cells are then incubated in Draq5 1/200 dilution for 5 minutes on ice. Draq5+/mCherry+ cells were sorted by the Stowers Institute Cytometry Core Facility using a BD Influx Cell Sorter BD Biosciences  San Jose  CA. USA  with cells collected in tubes containing 10mL 1XDPBS/0.04% BSA. Cells were not fixed in methanol as in previous protocols as we found this gave inconsistent results with 10X Genomics version 3 kits. Sorted cells are then spun down at 350rcf at 4oC for 2 min in a swinging bucket centrifuge with slow deceleration. Most of the supernatant is removed and the cells are resuspended in approximately remaining 100mL. Cells deemed to be at least 80% viable were loaded based on live cell concentration onto a Chromium X Series instrument 10x Genomics and libraries prepared using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 10x Genomics according to manufacturer\u2019s directions. Resulting cDNA and short fragment libraries were checked for quality and quantity using a 2100 Bioanalyzer Agilent Technologies and Qubit Fluorometer Thermo Fisher Scientific. With cells captured estimated at 6 800 9 600 cells per sample  libraries were pooled and sequenced to a depth necessary to achieve at least 30 000 mean reads per cell on an Illumina NextSeq 2000 instrument utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths: 28*10*10*90bp. scRNA seq 10x Genomics", "5dpf zebrafish FACS sorted lateral line cells were used. Standard growing condition were used.", "cell type:Homostasis|genotype:Wildtype", "GSM8288755", "GSM8288755: ccndx sibling1; Danio rerio; RNA Seq", "GSM8288755 r1", "GSM8288755", "1", "5 dpf zebrafish were anesthetized with Tricane then split between two 70mm cell strainers Falcon and placed in 0.25% Trypsin EDTA Gibco on ice. The larvae from each strainer are then added to a 5ml round bottom tube Falcon and the tissue is broken up via slowly pipetting up and down using a pipette man and a glass pipette VWR keeping the tubes on ice. The total time from placing larvae in trypsin to finishing pipetting is approximately 8 minutes. The tissue is then filtered through 70mm filter BD Biosciences  pelleted for 5 min at 2000rpm at 4oC and then the pellet is resuspended in 1xDPBS/0.04%BSA. The pelleting and resuspension in 1xDPBS/0.04%BSA is repeated two more times. post the final pellet the cells are resuspended in 0.5mL 1xDPBS/0.04%BSA then cells are combined and put through another 70mm filter into a 5ml round bottom tube. Cells are then incubated in Draq5 1/200 dilution for 5 minutes on ice. Draq5+/mCherry+ cells were sorted by the Stowers Institute Cytometry Core Facility using a BD Influx Cell Sorter BD Biosciences  San Jose  CA. USA  with cells collected in tubes containing 10mL 1XDPBS/0.04% BSA. Cells were not fixed in methanol as in previous protocols as we found this gave inconsistent results with 10X Genomics version 3 kits. Sorted cells are then spun down at 350rcf at 4oC for 2 min in a swinging bucket centrifuge with slow deceleration. Most of the supernatant is removed and the cells are resuspended in approximately remaining 100mL. Cells deemed to be at least 80% viable were loaded based on live cell concentration onto a Chromium X Series instrument 10x Genomics and libraries prepared using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 10x Genomics according to manufacturer's directions. Resulting cDNA and short fragment libraries were checked for quality and quantity using a 2100 Bioanalyzer Agilent Technologies and Qubit Fluorometer Thermo Fisher Scientific. With cells captured estimated at 6 800 9 600 cells per sample  libraries were pooled and sequenced to a depth necessary to achieve at least 30 000 mean reads per cell on an Illumina NextSeq 2000 instrument utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths: 28*10*10*90bp. scRNA seq 10x Genomics", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP509548", null, "assembly:danRer11|intentional duplicate", "ccndx_sibling1.bam", "10X Genomics bam file", 27531756630.0, 305908407.0, "GSM8288755 r1", "0:90", "A:8252775526;C:5615092533;G:6288684779;T:7373374402;N:1829390", 90, null, null, null, 8252775526, 5615092533, 6288684779, 7373374402, 1829390, "SRX24673328", "SRS21408056", "SRA1876130", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", 1, 0.92077, null, 0.29182, null, 0.76524, null, 0.53575, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-05-23", "Larval", "Larval", "Lateral Line", "Sensory System"], [32368, "SRR29152189", "SRX24673327", "SRS21408059", "SRP509548", "PRJNA1115803", "Stem and progenitor cell proliferation are independently regulated by cell type specific cyclinD genes", "GSE268255", "Transcriptome Analysis", "Regeneration and homeostatic turnover of solid tissues depend on the proliferation of symmetrically dividing adult stem cells  which either remain stem cells or differentiate based on their niche position. Here we demonstrate that in zebrafish lateral line sensory organs  stem and progenitor cell proliferation are independently regulated by two cyclinD genes. Loss of ccnd2a impairs stem cell proliferation during development  while loss of ccndx disrupts hair cell progenitor proliferation but allows normal differentiation. Notably  ccnd2a can functionally replace ccndx  indicating that the respective effects of these Cyclins on proliferation are due to cell type specific expression. However  even though hair cell progenitors differentiate normally in ccndx mutants  they are mispolarized due to hes2 and Emx2 downregulation. Thus  regulated proliferation ensures that equal numbers of hair cells are polarized in opposite directions. Our study reveals cell type specific roles for cyclinD genes in regulating the different populations of symmetrically dividing cells governing organ development and regeneration  with implications for regenerative medicine and disease. Overall design: Two replicates per sibling or ccndx mutant were used", null, null, null, "ccndx mutant2", "GSM8288754", null, "tissue:5dpf zebrafish FACS sorted lateral line cells|cell type:Homostasis|genotype:Mutant|geo loc name:missing|collection date:missing", "ccndx mutant2", "Raw sequencing data were processed using 10X Genomics Cell Ranger pipeline. Reads were demultiplexed into Fastq file format using cellranger mkfastq. Genome index was built by cellranger mkref using zebrafish genome danRer11  ensembl 98 gene model. Data were aligned by STAR aligner and cell counts tables were generated using cellranger count function with default parameters. Assembly: danRer11 Supplementary files format and content: single cell  count matrix in hdf5 format  raw data in bam format.", "5dpf zebrafish FACS sorted lateral line cells", "All cells were collected during homeostasis  no treatments were performed.", "5 dpf zebrafish were anesthetized with Tricane then split between two 70mm cell strainers Falcon and placed in 0.25% Trypsin EDTA Gibco on ice. The larvae from each strainer are then added to a 5ml round bottom tube Falcon and the tissue is broken up via slowly pipetting up and down using a pipette man and a glass pipette VWR keeping the tubes on ice. The total time from placing larvae in trypsin to finishing pipetting is approximately 8 minutes. The tissue is then filtered through 70mm filter BD Biosciences  pelleted for 5 min at 2000rpm at 4oC and then the pellet is resuspended in 1xDPBS/0.04%BSA. The pelleting and resuspension in 1xDPBS/0.04%BSA is repeated two more times. post the final pellet the cells are resuspended in 0.5mL 1xDPBS/0.04%BSA then cells are combined and put through another 70mm filter into a 5ml round bottom tube. Cells are then incubated in Draq5 1/200 dilution for 5 minutes on ice. Draq5+/mCherry+ cells were sorted by the Stowers Institute Cytometry Core Facility using a BD Influx Cell Sorter BD Biosciences  San Jose  CA. USA  with cells collected in tubes containing 10mL 1XDPBS/0.04% BSA. Cells were not fixed in methanol as in previous protocols as we found this gave inconsistent results with 10X Genomics version 3 kits. Sorted cells are then spun down at 350rcf at 4oC for 2 min in a swinging bucket centrifuge with slow deceleration. Most of the supernatant is removed and the cells are resuspended in approximately remaining 100mL. Cells deemed to be at least 80% viable were loaded based on live cell concentration onto a Chromium X Series instrument 10x Genomics and libraries prepared using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 10x Genomics according to manufacturer\u2019s directions. Resulting cDNA and short fragment libraries were checked for quality and quantity using a 2100 Bioanalyzer Agilent Technologies and Qubit Fluorometer Thermo Fisher Scientific. With cells captured estimated at 6 800 9 600 cells per sample  libraries were pooled and sequenced to a depth necessary to achieve at least 30 000 mean reads per cell on an Illumina NextSeq 2000 instrument utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths: 28*10*10*90bp. scRNA seq 10x Genomics", "5dpf zebrafish FACS sorted lateral line cells were used. Standard growing condition were used.", "cell type:Homostasis|genotype:Mutant", "GSM8288754", "GSM8288754: ccndx mutant2; Danio rerio; RNA Seq", "GSM8288754 r1", "GSM8288754", "1", "5 dpf zebrafish were anesthetized with Tricane then split between two 70mm cell strainers Falcon and placed in 0.25% Trypsin EDTA Gibco on ice. The larvae from each strainer are then added to a 5ml round bottom tube Falcon and the tissue is broken up via slowly pipetting up and down using a pipette man and a glass pipette VWR keeping the tubes on ice. The total time from placing larvae in trypsin to finishing pipetting is approximately 8 minutes. The tissue is then filtered through 70mm filter BD Biosciences  pelleted for 5 min at 2000rpm at 4oC and then the pellet is resuspended in 1xDPBS/0.04%BSA. The pelleting and resuspension in 1xDPBS/0.04%BSA is repeated two more times. post the final pellet the cells are resuspended in 0.5mL 1xDPBS/0.04%BSA then cells are combined and put through another 70mm filter into a 5ml round bottom tube. Cells are then incubated in Draq5 1/200 dilution for 5 minutes on ice. Draq5+/mCherry+ cells were sorted by the Stowers Institute Cytometry Core Facility using a BD Influx Cell Sorter BD Biosciences  San Jose  CA. USA  with cells collected in tubes containing 10mL 1XDPBS/0.04% BSA. Cells were not fixed in methanol as in previous protocols as we found this gave inconsistent results with 10X Genomics version 3 kits. Sorted cells are then spun down at 350rcf at 4oC for 2 min in a swinging bucket centrifuge with slow deceleration. Most of the supernatant is removed and the cells are resuspended in approximately remaining 100mL. Cells deemed to be at least 80% viable were loaded based on live cell concentration onto a Chromium X Series instrument 10x Genomics and libraries prepared using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 10x Genomics according to manufacturer's directions. Resulting cDNA and short fragment libraries were checked for quality and quantity using a 2100 Bioanalyzer Agilent Technologies and Qubit Fluorometer Thermo Fisher Scientific. With cells captured estimated at 6 800 9 600 cells per sample  libraries were pooled and sequenced to a depth necessary to achieve at least 30 000 mean reads per cell on an Illumina NextSeq 2000 instrument utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths: 28*10*10*90bp. scRNA seq 10x Genomics", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP509548", null, "assembly:danRer11|intentional duplicate", "ccndx_mutant2.bam", "10X Genomics bam file", 24590059740.0, 273222886.0, "GSM8288754 r1", "0:90", "A:6996284463;C:5349540108;G:5922688427;T:6319952971;N:1593771", 90, null, null, null, 6996284463, 5349540108, 5922688427, 6319952971, 1593771, "SRX24673327", "SRS21408059", "SRA1876130", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", 1, 0.94389, null, 0.21693, null, 0.75426, null, 0.54926, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-05-23", "Larval", "Larval", "Lateral Line", "Sensory System"], [32369, "SRR29152190", "SRX24673326", "SRS21408058", "SRP509548", "PRJNA1115803", "Stem and progenitor cell proliferation are independently regulated by cell type specific cyclinD genes", "GSE268255", "Transcriptome Analysis", "Regeneration and homeostatic turnover of solid tissues depend on the proliferation of symmetrically dividing adult stem cells  which either remain stem cells or differentiate based on their niche position. Here we demonstrate that in zebrafish lateral line sensory organs  stem and progenitor cell proliferation are independently regulated by two cyclinD genes. Loss of ccnd2a impairs stem cell proliferation during development  while loss of ccndx disrupts hair cell progenitor proliferation but allows normal differentiation. Notably  ccnd2a can functionally replace ccndx  indicating that the respective effects of these Cyclins on proliferation are due to cell type specific expression. However  even though hair cell progenitors differentiate normally in ccndx mutants  they are mispolarized due to hes2 and Emx2 downregulation. Thus  regulated proliferation ensures that equal numbers of hair cells are polarized in opposite directions. Our study reveals cell type specific roles for cyclinD genes in regulating the different populations of symmetrically dividing cells governing organ development and regeneration  with implications for regenerative medicine and disease. Overall design: Two replicates per sibling or ccndx mutant were used", null, null, null, "ccndx mutant1", "GSM8288753", null, "tissue:5dpf zebrafish FACS sorted lateral line cells|cell type:Homostasis|genotype:Mutant|geo loc name:missing|collection date:missing", "ccndx mutant1", "Raw sequencing data were processed using 10X Genomics Cell Ranger pipeline. Reads were demultiplexed into Fastq file format using cellranger mkfastq. Genome index was built by cellranger mkref using zebrafish genome danRer11  ensembl 98 gene model. Data were aligned by STAR aligner and cell counts tables were generated using cellranger count function with default parameters. Assembly: danRer11 Supplementary files format and content: single cell  count matrix in hdf5 format  raw data in bam format.", "5dpf zebrafish FACS sorted lateral line cells", "All cells were collected during homeostasis  no treatments were performed.", "5 dpf zebrafish were anesthetized with Tricane then split between two 70mm cell strainers Falcon and placed in 0.25% Trypsin EDTA Gibco on ice. The larvae from each strainer are then added to a 5ml round bottom tube Falcon and the tissue is broken up via slowly pipetting up and down using a pipette man and a glass pipette VWR keeping the tubes on ice. The total time from placing larvae in trypsin to finishing pipetting is approximately 8 minutes. The tissue is then filtered through 70mm filter BD Biosciences  pelleted for 5 min at 2000rpm at 4oC and then the pellet is resuspended in 1xDPBS/0.04%BSA. The pelleting and resuspension in 1xDPBS/0.04%BSA is repeated two more times. post the final pellet the cells are resuspended in 0.5mL 1xDPBS/0.04%BSA then cells are combined and put through another 70mm filter into a 5ml round bottom tube. Cells are then incubated in Draq5 1/200 dilution for 5 minutes on ice. Draq5+/mCherry+ cells were sorted by the Stowers Institute Cytometry Core Facility using a BD Influx Cell Sorter BD Biosciences  San Jose  CA. USA  with cells collected in tubes containing 10mL 1XDPBS/0.04% BSA. Cells were not fixed in methanol as in previous protocols as we found this gave inconsistent results with 10X Genomics version 3 kits. Sorted cells are then spun down at 350rcf at 4oC for 2 min in a swinging bucket centrifuge with slow deceleration. Most of the supernatant is removed and the cells are resuspended in approximately remaining 100mL. Cells deemed to be at least 80% viable were loaded based on live cell concentration onto a Chromium X Series instrument 10x Genomics and libraries prepared using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 10x Genomics according to manufacturer\u2019s directions. Resulting cDNA and short fragment libraries were checked for quality and quantity using a 2100 Bioanalyzer Agilent Technologies and Qubit Fluorometer Thermo Fisher Scientific. With cells captured estimated at 6 800 9 600 cells per sample  libraries were pooled and sequenced to a depth necessary to achieve at least 30 000 mean reads per cell on an Illumina NextSeq 2000 instrument utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths: 28*10*10*90bp. scRNA seq 10x Genomics", "5dpf zebrafish FACS sorted lateral line cells were used. Standard growing condition were used.", "cell type:Homostasis|genotype:Mutant", "GSM8288753", "GSM8288753: ccndx mutant1; Danio rerio; RNA Seq", "GSM8288753 r1", "GSM8288753", "1", "5 dpf zebrafish were anesthetized with Tricane then split between two 70mm cell strainers Falcon and placed in 0.25% Trypsin EDTA Gibco on ice. The larvae from each strainer are then added to a 5ml round bottom tube Falcon and the tissue is broken up via slowly pipetting up and down using a pipette man and a glass pipette VWR keeping the tubes on ice. The total time from placing larvae in trypsin to finishing pipetting is approximately 8 minutes. The tissue is then filtered through 70mm filter BD Biosciences  pelleted for 5 min at 2000rpm at 4oC and then the pellet is resuspended in 1xDPBS/0.04%BSA. The pelleting and resuspension in 1xDPBS/0.04%BSA is repeated two more times. post the final pellet the cells are resuspended in 0.5mL 1xDPBS/0.04%BSA then cells are combined and put through another 70mm filter into a 5ml round bottom tube. Cells are then incubated in Draq5 1/200 dilution for 5 minutes on ice. Draq5+/mCherry+ cells were sorted by the Stowers Institute Cytometry Core Facility using a BD Influx Cell Sorter BD Biosciences  San Jose  CA. USA  with cells collected in tubes containing 10mL 1XDPBS/0.04% BSA. Cells were not fixed in methanol as in previous protocols as we found this gave inconsistent results with 10X Genomics version 3 kits. Sorted cells are then spun down at 350rcf at 4oC for 2 min in a swinging bucket centrifuge with slow deceleration. Most of the supernatant is removed and the cells are resuspended in approximately remaining 100mL. Cells deemed to be at least 80% viable were loaded based on live cell concentration onto a Chromium X Series instrument 10x Genomics and libraries prepared using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 10x Genomics according to manufacturer's directions. Resulting cDNA and short fragment libraries were checked for quality and quantity using a 2100 Bioanalyzer Agilent Technologies and Qubit Fluorometer Thermo Fisher Scientific. With cells captured estimated at 6 800 9 600 cells per sample  libraries were pooled and sequenced to a depth necessary to achieve at least 30 000 mean reads per cell on an Illumina NextSeq 2000 instrument utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths: 28*10*10*90bp. scRNA seq 10x Genomics", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP509548", null, "assembly:danRer11|intentional duplicate", "ccndx_mutant1.bam", "10X Genomics bam file", 29191358880.0, 324348432.0, "GSM8288753 r1", "0:90", "A:8805522313;C:5925846684;G:6724305340;T:7733851337;N:1833206", 90, null, null, null, 8805522313, 5925846684, 6724305340, 7733851337, 1833206, "SRX24673326", "SRS21408058", "SRA1876130", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", 1, 0.91635, null, 0.28762, null, 0.77488, null, 0.56058, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-05-23", "Larval", "Larval", "Lateral Line", "Sensory System"], [50723, "SRR8270602", "SRX5087288", "SRS4099391", "SRP171998", "PRJNA507898", "Single cell RNA Seq reveals Fgf signaling dynamics during sensory hair cell regeneration", "GSE123241", "Transcriptome Analysis", "Loss of sensory hair cells leads to deafness and balance deficiencies. In contrast to mammalian hair cells  zebrafish ear and lateral line hair cells regenerate from poorly characterized  proliferating support cells. Equally ill defined is the gene regulatory network underlying the progression of support cells to cycling hair cell progenitors and differentiated hair cells. We used single cell RNA Sequencing scRNA Seq of lateral line sensory organs and uncovered five different support cell types  including quiescent and activated stem cells. In silico ordering of support cells along a developmental trajectory identified cells that self renew and new groups of genes required for hair cell differentiation. scRNA Seq analyses of fgf3 mutants  in which hair cell regeneration is increased demonstrates that Fgf and Notch signaling inhibit proliferation of support cells in parallel by inhibiting Wnt signaling. Our scRNA Seq analyses set the foundation for mechanistic studies of sensory organ regeneration and is crucial for identifying factors to trigger hair cell production in mammals. Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 3 different samples: wild type  fgf3 mutants  and fgf3 siblings.", null, "pubmed:30681411;pubmed:31488837", null, "fgf3 mutant", "GSM3498554", null, "source name:neuromast|age:5dpf|tissue:neuromast|genotype:fgf3 / |strain:fgf3^t26212; ETkrt4:EGFPSqGw57A; Tgpou4f3:GAP GFPs356t screened for mutants", "fgf3 mutant", "Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.", "neuromast", null, "Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq", null, "age:5dpf|tissue:neuromast|genotype:fgf3 / |strain:fgf3^t26212;ETkrt4:EGFPSqGw57A;Tgpou4f3:GAP GFPs356t screened for mutants", "GSM3498554", "GSM3498554: fgf3 mutant; Danio rerio; RNA Seq", "GSM3498554", null, "1", "Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq", "GEO Accession:GSM3498554", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP171998", null, null, "possorted_genome_bam_fgf3_mut.bam", "10X Genomics bam file", 16974126576.0, 171455824.0, "GSM3498554 r1", "0:99", "A:5250835858;C:3266700009;G:3497115040;T:4840312852;N:119162817", 99, null, null, null, 5250835858, 3266700009, 3497115040, 4840312852, 119162817, "SRX5087288", "SRS4099391", "SRA817952", "GEO", "Stowers Institute", 1, 0.89941, null, 0.21879, null, 0.80805, null, 0.48702, null, 99, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2018-12-02", "Larval", "Larval", "Lateral Line", "Sensory System"], [50724, "SRR8270601", "SRX5087287", "SRS4099390", "SRP171998", "PRJNA507898", "Single cell RNA Seq reveals Fgf signaling dynamics during sensory hair cell regeneration", "GSE123241", "Transcriptome Analysis", "Loss of sensory hair cells leads to deafness and balance deficiencies. In contrast to mammalian hair cells  zebrafish ear and lateral line hair cells regenerate from poorly characterized  proliferating support cells. Equally ill defined is the gene regulatory network underlying the progression of support cells to cycling hair cell progenitors and differentiated hair cells. We used single cell RNA Sequencing scRNA Seq of lateral line sensory organs and uncovered five different support cell types  including quiescent and activated stem cells. In silico ordering of support cells along a developmental trajectory identified cells that self renew and new groups of genes required for hair cell differentiation. scRNA Seq analyses of fgf3 mutants  in which hair cell regeneration is increased demonstrates that Fgf and Notch signaling inhibit proliferation of support cells in parallel by inhibiting Wnt signaling. Our scRNA Seq analyses set the foundation for mechanistic studies of sensory organ regeneration and is crucial for identifying factors to trigger hair cell production in mammals. Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 3 different samples: wild type  fgf3 mutants  and fgf3 siblings.", null, "pubmed:30681411;pubmed:31488837", null, "fgf3 sibling", "GSM3498553", null, "source name:neuromast|age:5dpf|tissue:neuromast|genotype:fgf3+/ |strain:fgf3^t26212; ETkrt4:EGFPSqGw57A; Tgpou4f3:GAP GFPs356t", "fgf3 sibling", "Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.", "neuromast", null, "Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq", null, "age:5dpf|tissue:neuromast|genotype:fgf3+/ |strain:fgf3^t26212;ETkrt4:EGFPSqGw57A;Tgpou4f3:GAP GFPs356t", "GSM3498553", "GSM3498553: fgf3 sibling; Danio rerio; RNA Seq", "GSM3498553", null, "1", "Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq", "GEO Accession:GSM3498553", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP171998", null, null, "possorted_genome_bam_fgf3_sib.bam", "10X Genomics bam file", 15833733894.0, 159936706.0, "GSM3498553 r1", "0:99", "A:4876827108;C:3036857735;G:3248946665;T:4560644612;N:110457774", 99, null, null, null, 4876827108, 3036857735, 3248946665, 4560644612, 110457774, "SRX5087287", "SRS4099390", "SRA817952", "GEO", "Stowers Institute", 1, 0.89735, null, 0.21699, null, 0.80409, null, 0.4894, null, 99, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2018-12-02", "Larval", "Larval", "Lateral Line", "Sensory System"], [50725, "SRR8270600", "SRX5087286", "SRS4099389", "SRP171998", "PRJNA507898", "Single cell RNA Seq reveals Fgf signaling dynamics during sensory hair cell regeneration", "GSE123241", "Transcriptome Analysis", "Loss of sensory hair cells leads to deafness and balance deficiencies. In contrast to mammalian hair cells  zebrafish ear and lateral line hair cells regenerate from poorly characterized  proliferating support cells. Equally ill defined is the gene regulatory network underlying the progression of support cells to cycling hair cell progenitors and differentiated hair cells. We used single cell RNA Sequencing scRNA Seq of lateral line sensory organs and uncovered five different support cell types  including quiescent and activated stem cells. In silico ordering of support cells along a developmental trajectory identified cells that self renew and new groups of genes required for hair cell differentiation. scRNA Seq analyses of fgf3 mutants  in which hair cell regeneration is increased demonstrates that Fgf and Notch signaling inhibit proliferation of support cells in parallel by inhibiting Wnt signaling. Our scRNA Seq analyses set the foundation for mechanistic studies of sensory organ regeneration and is crucial for identifying factors to trigger hair cell production in mammals. Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 3 different samples: wild type  fgf3 mutants  and fgf3 siblings.", null, "pubmed:30681411;pubmed:31488837", null, "WT", "GSM3498552", null, "source name:neuromast|age:5dpf|tissue:neuromast|genotype:WT|strain:ETkrt4:EGFPSqGw57A; Tgpou4f3:GAP GFPs356t", "WT", "Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.", "neuromast", null, "Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq", null, "age:5dpf|tissue:neuromast|genotype:WT|strain:ETkrt4:EGFPSqGw57A;Tgpou4f3:GAP GFPs356t", "GSM3498552", "GSM3498552: WT; Danio rerio; RNA Seq", "GSM3498552", null, "1", "Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq", "GEO Accession:GSM3498552", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP171998", null, null, "possorted_genome_bam_WT.bam", "10X Genomics bam file", 32918660478.0, 332511722.0, "GSM3498552 r1", "0:99", "A:10031241232;C:6365493396;G:6804558002;T:9674542542;N:42825306", 99, null, null, null, 10031241232, 6365493396, 6804558002, 9674542542, 42825306, "SRX5087286", "SRS4099389", "SRA817952", "GEO", "Stowers Institute", 1, 0.90685, null, 0.26503, null, 0.79368, null, 0.47639, null, 99, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2018-12-02", "Larval", "Larval", "Lateral Line", "Sensory System"], [56605, "SRR11031290", "SRX7683557", "SRS6110537", "SRP247442", "PRJNA605021", "Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2", "GSE144827", "Transcriptome Analysis", "This dataset consists of single cell RNA seq 10X data of neuromast cells from zebrafish larvae. Posterior lateral line neuromast cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs  and from Tg[Etkrt4:EGFPsqgw57A] larvae expressing EGFP in supporting cells. Overall design: A single cell RNA seq experiment of isolated neuromast cells from zebrafish larvae was performed using 10X Genomics technology to generate single cell transcriptomic profiles of supporting cells and hair cells.", null, "pubmed:32109392", null, "hair cells", "GSM4298909", null, "source name:zebrafish neuromast cells|genotype:Tg[myo6b:actb1 EGFP]|source tissue:neuromast|developmental day:7 dpf", "hair cells", "The 10X Genomics core computational software Cellranger v.2.1.1 was used for alignment and processing of next generation sequencing reads of the scRNA seq data as recommended https://support.10xgenomics.com/single cell gene expression/software/overview/welcome. Genome build: GRCz11 Supplementary files format and content: Raw UMI count matrix feature x cell barcode from 10X Genomics single cell RNAseq experiments. gzipped files contains count matrix in market matrix format  cell barcodes as tab delimited text file and feature names as tab delimited text file.", "zebrafish neuromast cells", "none", "Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. Single cell libraries were generated using the ChromiumTM Single cell 3`library and gel bead kit v2 PN #120237 from 10x Genomics. Libraries were sequenced on the HiSeq4000 Illumina with 150bp paired end sequencing. RNA Seq 10X Genomics", "Standardized conditions at 28.5\u00b0C in the 0 3 x Danieau\u2019s solution.", "genotype:Tg[myo6b:actb1 EGFP]|source tissue:neuromast|developmental day:7 dpf", "GSM4298909", "GSM4298909: hair cells; Danio rerio; RNA Seq", "GSM4298909", null, "1", "Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. Single cell libraries were generated using the ChromiumTM Single cell 3`library and gel bead kit v2 PN #120237 from 10x Genomics. Libraries were sequenced on the HiSeq4000 Illumina with 150bp paired end sequencing. RNA Seq 10X Genomics", "GEO Accession:GSM4298909", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP247442", null, null, "hair_cells_R2.fastq.gz hair_cells_R1.fastq.gz", "fastq fastq", 89474157378.0, 505503714.0, "GSM4298909 r1", "0:26 1:151", "A:25071099481;C:19794086212;G:19845960995;T:24749018204;N:13992486", 26, 151, null, null, 25071099481, 19794086212, 19845960995, 24749018204, 13992486, "SRX7683557", "SRS6110537", "SRA1038640", "GEO", "Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum M\u00fcnchen", 2, 0.00294, 0.9352, 0.00072, 0.07461, 0.99358, 0.81487, 0.46744, 0.43177, 26, 151, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-02-05", "Larval", "Larval", "Lateral Line", "Sensory System"], [56606, "SRR11031289", "SRX7683556", "SRS6110536", "SRP247442", "PRJNA605021", "Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2", "GSE144827", "Transcriptome Analysis", "This dataset consists of single cell RNA seq 10X data of neuromast cells from zebrafish larvae. Posterior lateral line neuromast cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs  and from Tg[Etkrt4:EGFPsqgw57A] larvae expressing EGFP in supporting cells. Overall design: A single cell RNA seq experiment of isolated neuromast cells from zebrafish larvae was performed using 10X Genomics technology to generate single cell transcriptomic profiles of supporting cells and hair cells.", null, "pubmed:32109392", null, "supporting cells", "GSM4298908", null, "source name:zebrafish neuromast cells|genotype:Tg[Etkrt4:EGFPsqgw57A]|source tissue:neuromast|developmental day:7 dpf", "supporting cells", "The 10X Genomics core computational software Cellranger v.2.1.1 was used for alignment and processing of next generation sequencing reads of the scRNA seq data as recommended https://support.10xgenomics.com/single cell gene expression/software/overview/welcome. Genome build: GRCz11 Supplementary files format and content: Raw UMI count matrix feature x cell barcode from 10X Genomics single cell RNAseq experiments. gzipped files contains count matrix in market matrix format  cell barcodes as tab delimited text file and feature names as tab delimited text file.", "zebrafish neuromast cells", "none", "Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. Single cell libraries were generated using the ChromiumTM Single cell 3`library and gel bead kit v2 PN #120237 from 10x Genomics. Libraries were sequenced on the HiSeq4000 Illumina with 150bp paired end sequencing. RNA Seq 10X Genomics", "Standardized conditions at 28.5\u00b0C in the 0 3 x Danieau\u2019s solution.", "genotype:Tg[Etkrt4:EGFPsqgw57A]|source tissue:neuromast|developmental day:7 dpf", "GSM4298908", "GSM4298908: supporting cells; Danio rerio; RNA Seq", "GSM4298908", null, "1", "Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. Single cell libraries were generated using the ChromiumTM Single cell 3`library and gel bead kit v2 PN #120237 from 10x Genomics. Libraries were sequenced on the HiSeq4000 Illumina with 150bp paired end sequencing. RNA Seq 10X Genomics", "GEO Accession:GSM4298908", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP247442", null, null, "support_cells_R2.fastq.gz support_cells_R1.fastq.gz", "fastq fastq", 209506251249.0, 1183651137.0, "GSM4298908 r1", "0:26 1:151", "A:59676591457;C:46803384480;G:47908589489;T:55084749523;N:32936300", 26, 151, null, null, 59676591457, 46803384480, 47908589489, 55084749523, 32936300, "SRX7683556", "SRS6110536", "SRA1038640", "GEO", "Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum M\u00fcnchen", 2, 0.00206, 0.92892, 0.00042, 0.04303, 0.99508, 0.86354, 0.40312, 0.45704, 26, 151, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2020-02-05", "Larval", "Larval", "Lateral Line", "Sensory System"], [68516, "SRR17900890", "SRX14059608", "SRS11892528", "SRP358576", "PRJNA803902", "High resolution single cell transcriptome analysis of zebrafish sensory hair cell regeneration", "GSE196211", "Transcriptome Analysis", "NOT PROVIDED; REQUESTED Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 7 different samples: homeo  0min post neomycin  30min 1hr  3hr  5hr  10hr", null, "pubmed:35316618", null, "10hr post neomycin", "GSM5862805", null, "source name:neuromast|age:5dpf|tissue:neuromast|treatment/time point:10hr post neomycin|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP", "10hr post neomycin", "Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10  ensembl release 91  using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.", "neuromast", null, "Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq", null, "age:5dpf|tissue:neuromast|treatment/time point:10hr post neomycin|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP", "GSM5862805", "GSM5862805: 10hr post neomycin; Danio rerio; RNA Seq", "GSM5862805 r1", "GSM5862805", "1", "Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP358576", null, "assembly:danRer10|intentional duplicate", "10hr_possorted_genome_bam.bam", "10X Genomics bam file", 11755529379.0, 118742721.0, "GSM5862805 r1", "0:99", "A:3815855652;C:2300159508;G:2649552225;T:2989724050;N:237944", 99, null, null, null, 3815855652, 2300159508, 2649552225, 2989724050, 237944, "SRX14059608", "SRS11892528", "SRA1367859", "Piotrowski Lab, Stowers Institute for Medical Research", "Piotrowski Lab, Stowers Institute for Medical Research", 1, 0.88584, null, 0.18938, null, 0.81968, null, 0.57795, null, 99, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-02-06", "Larval", "Larval", "Lateral Line", "Sensory System"], [68517, "SRR17900891", "SRX14059607", "SRS11892527", "SRP358576", "PRJNA803902", "High resolution single cell transcriptome analysis of zebrafish sensory hair cell regeneration", "GSE196211", "Transcriptome Analysis", "NOT PROVIDED; REQUESTED Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 7 different samples: homeo  0min post neomycin  30min 1hr  3hr  5hr  10hr", null, "pubmed:35316618", null, "5hr post neomycin", "GSM5862804", null, "source name:neuromast|age:5dpf|tissue:neuromast|treatment/time point:5hr post neomycin|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP", "5hr post neomycin", "Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10  ensembl release 91  using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.", "neuromast", null, "Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq", null, "age:5dpf|tissue:neuromast|treatment/time point:5hr post neomycin|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP", "GSM5862804", "GSM5862804: 5hr post neomycin; Danio rerio; RNA Seq", "GSM5862804 r1", "GSM5862804", "1", "Presumptive neuromast cells GFP+ were isolated by FACS. 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Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.", "neuromast", null, "Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq", null, "age:5dpf|tissue:neuromast|treatment/time point:3hr post neomycin|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP", "GSM5862803", "GSM5862803: 3hr post neomycin; Danio rerio; RNA Seq", "GSM5862803 r1", "GSM5862803", "1", "Presumptive neuromast cells GFP+ were isolated by FACS. 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