metadata: run_metadata: 16 rows where experiment.platform = "ILLUMINA", technology = "10x" and tissue

16 rows where experiment.platform = "ILLUMINA", technology = "10x" and tissue_curation = "Lateral Line"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	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.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
32366	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		ccndx sibling2	GSM8288756	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’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 nec…	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 nec…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP509548	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		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		0.20814		0.75452		0.52756		90		B		usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Larval	Larval	Lateral Line	Sensory System
32367	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		ccndx sibling1	GSM8288755	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’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 nec…	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 nec…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP509548	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		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		0.29182		0.76524		0.53575		90		B		usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Larval	Larval	Lateral Line	Sensory System
32368	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		ccndx mutant2	GSM8288754	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’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 nec…	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 nec…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP509548	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		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		0.21693		0.75426		0.54926		90		B		usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Larval	Larval	Lateral Line	Sensory System
32369	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		ccndx mutant1	GSM8288753	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’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 nec…	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 nec…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP509548	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		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		0.28762		0.77488		0.56058		90		B		usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Larval	Larval	Lateral Line	Sensory System
50723	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.	pubmed:30681411;pubmed:31488837	fgf3 mutant	GSM3498554	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		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		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		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	SRP171998		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		5250835858	3266700009	3497115040	4840312852	119162817	SRX5087288	SRS4099391	SRA817952	GEO	Stowers Institute	1	0.89941		0.21879		0.80805		0.48702		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2018-12-02	Larval	Larval	Lateral Line	Sensory System
50724	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.	pubmed:30681411;pubmed:31488837	fgf3 sibling	GSM3498553	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		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		age:5dpf\|tissue:neuromast\|genotype:fgf3+/ \|strain:fgf3^t26212;ETkrt4:EGFPSqGw57A;Tgpou4f3:GAP GFPs356t	GSM3498553	GSM3498553: fgf3 sibling; Danio rerio; RNA Seq	GSM3498553		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	SRP171998		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		4876827108	3036857735	3248946665	4560644612	110457774	SRX5087287	SRS4099390	SRA817952	GEO	Stowers Institute	1	0.89735		0.21699		0.80409		0.4894		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2018-12-02	Larval	Larval	Lateral Line	Sensory System
50725	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.	pubmed:30681411;pubmed:31488837	WT	GSM3498552	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		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		age:5dpf\|tissue:neuromast\|genotype:WT\|strain:ETkrt4:EGFPSqGw57A;Tgpou4f3:GAP GFPs356t	GSM3498552	GSM3498552: WT; Danio rerio; RNA Seq	GSM3498552		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	SRP171998		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		10031241232	6365493396	6804558002	9674542542	42825306	SRX5087286	SRS4099389	SRA817952	GEO	Stowers Institute	1	0.90685		0.26503		0.79368		0.47639		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2018-12-02	Larval	Larval	Lateral Line	Sensory System
56605	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.	pubmed:32109392	hair cells	GSM4298909	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°C in the 0 3 x Danieau’s solution.	genotype:Tg[myo6b:actb1 EGFP]\|source tissue:neuromast\|developmental day:7 dpf	GSM4298909	GSM4298909: hair cells; Danio rerio; RNA Seq	GSM4298909		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	SRP247442		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	25071099481	19794086212	19845960995	24749018204	13992486	SRX7683557	SRS6110537	SRA1038640	GEO	Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München	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	Germany	2020-02-05	Larval	Larval	Lateral Line	Sensory System
56606	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.	pubmed:32109392	supporting cells	GSM4298908	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°C in the 0 3 x Danieau’s solution.	genotype:Tg[Etkrt4:EGFPsqgw57A]\|source tissue:neuromast\|developmental day:7 dpf	GSM4298908	GSM4298908: supporting cells; Danio rerio; RNA Seq	GSM4298908		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	SRP247442		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	59676591457	46803384480	47908589489	55084749523	32936300	SRX7683556	SRS6110536	SRA1038640	GEO	Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München	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	Germany	2020-02-05	Larval	Larval	Lateral Line	Sensory System
68516	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	pubmed:35316618	10hr post neomycin	GSM5862805	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		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		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		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP358576	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		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		0.18938		0.81968		0.57795		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-02-06	Larval	Larval	Lateral Line	Sensory System
68517	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	pubmed:35316618	5hr post neomycin	GSM5862804	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		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		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. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP358576	assembly:danRer10\|intentional duplicate	5hr_possorted_genome_bam.bam	10X Genomics bam file	10868082885.0	109778615.0	GSM5862804 r1	0:99	A:3267489116;C:2251000050;G:2404850523;T:2944522797;N:220399	99		3267489116	2251000050	2404850523	2944522797	220399	SRX14059607	SRS11892527	SRA1367859	Piotrowski Lab, Stowers Institute for Medical Research	Piotrowski Lab, Stowers Institute for Medical Research	1	0.93721		0.18379		0.81852		0.54714		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-02-06	Larval	Larval	Lateral Line	Sensory System
68518	68518	SRR17900892	SRX14059606	SRS11892526	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	pubmed:35316618	3hr post neomycin	GSM5862803	source name:neuromast\|age:5dpf\|tissue:neuromast\|treatment/time point:3hr post neomycin\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	3hr 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		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		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. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP358576	assembly:danRer10\|intentional duplicate	3hr_possorted_genome_bam.bam	10X Genomics bam file	30818123028.0	311294172.0	GSM5862803 r1	0:99	A:9348916523;C:6246488965;G:6684733854;T:8511548264;N:26435422	99		9348916523	6246488965	6684733854	8511548264	26435422	SRX14059606	SRS11892526	SRA1367859	Piotrowski Lab, Stowers Institute for Medical Research	Piotrowski Lab, Stowers Institute for Medical Research	1	0.92667		0.21879		0.80736		0.52626		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-02-06	Larval	Larval	Lateral Line	Sensory System
68519	68519	SRR17900893	SRX14059605	SRS11892525	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	pubmed:35316618	1hr post neomycin	GSM5862802	source name:neuromast\|age:5dpf\|tissue:neuromast\|treatment/time point:1hr post neomycin\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	1hr 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		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		age:5dpf\|tissue:neuromast\|treatment/time point:1hr post neomycin\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	GSM5862802	GSM5862802: 1hr post neomycin; Danio rerio; RNA Seq	GSM5862802 r1	GSM5862802	1	Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP358576	assembly:danRer10\|intentional duplicate	1hr_possorted_genome_bam.bam	10X Genomics bam file	17016505902.0	171883898.0	GSM5862802 r1	0:99	A:5220935048;C:3448280771;G:3717726451;T:4625338927;N:4224705	99		5220935048	3448280771	3717726451	4625338927	4224705	SRX14059605	SRS11892525	SRA1367859	Piotrowski Lab, Stowers Institute for Medical Research	Piotrowski Lab, Stowers Institute for Medical Research	1	0.92365		0.21642		0.83339		0.55101		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-02-06	Larval	Larval	Lateral Line	Sensory System
68520	68520	SRR17900894	SRX14059604	SRS11892524	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	pubmed:35316618	30min post neomycin	GSM5862801	source name:neuromast\|age:5dpf\|tissue:neuromast\|treatment/time point:30min post neomycin\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	30min 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		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		age:5dpf\|tissue:neuromast\|treatment/time point:30min post neomycin\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	GSM5862801	GSM5862801: 30min post neomycin; Danio rerio; RNA Seq	GSM5862801 r1	GSM5862801	1	Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP358576	assembly:danRer10\|intentional duplicate	30min_possorted_genome_bam.bam	10X Genomics bam file	15228653913.0	153824787.0	GSM5862801 r1	0:99	A:4774203586;C:3007224980;G:3233337864;T:4213847766;N:39717	99		4774203586	3007224980	3233337864	4213847766	39717	SRX14059604	SRS11892524	SRA1367859	Piotrowski Lab, Stowers Institute for Medical Research	Piotrowski Lab, Stowers Institute for Medical Research	1	0.92255		0.24454		0.83128		0.55089		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-02-06	Larval	Larval	Lateral Line	Sensory System
68521	68521	SRR17900895	SRX14059603	SRS11892523	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	pubmed:35316618	0min post neomycin	GSM5862800	source name:neuromast\|age:5dpf\|tissue:neuromast\|treatment/time point:0min post neomycin\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	0min 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		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		age:5dpf\|tissue:neuromast\|treatment/time point:0min post neomycin\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	GSM5862800	GSM5862800: 0min post neomycin; Danio rerio; RNA Seq	GSM5862800 r1	GSM5862800	1	Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP358576	assembly:danRer10\|intentional duplicate	0min_possorted_genome_bam.bam	10X Genomics bam file	16733371941.0	169023959.0	GSM5862800 r1	0:99	A:5247307437;C:3263851520;G:3538128507;T:4684038782;N:45695	99		5247307437	3263851520	3538128507	4684038782	45695	SRX14059603	SRS11892523	SRA1367859	Piotrowski Lab, Stowers Institute for Medical Research	Piotrowski Lab, Stowers Institute for Medical Research	1	0.91636		0.24042		0.82875		0.54973		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-02-06	Larval	Larval	Lateral Line	Sensory System
68522	68522	SRR17900896	SRX14059602	SRS11892522	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	pubmed:35316618	homeo	GSM5862799	source name:neuromast\|age:5dpf\|tissue:neuromast\|treatment/time point:homeo\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	homeo	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		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		age:5dpf\|tissue:neuromast\|treatment/time point:homeo\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	GSM5862799	GSM5862799: homeo; Danio rerio; RNA Seq	GSM5862799 r1	GSM5862799	1	Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP358576	assembly:danRer10\|intentional duplicate	homeo_possorted_genome_bam.bam	10X Genomics bam file	15150832686.0	153038714.0	GSM5862799 r1	0:99	A:4484040403;C:3115374217;G:3333967460;T:4132413883;N:85036723	99		4484040403	3115374217	3333967460	4132413883	85036723	SRX14059602	SRS11892522	SRA1367859	Piotrowski Lab, Stowers Institute for Medical Research	Piotrowski Lab, Stowers Institute for Medical Research	1	0.93926		0.18875		0.80762		0.50625		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-02-06	Larval	Larval	Lateral Line	Sensory System

Advanced export

JSON shape: default, array, newline-delimited

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