run_metadata
200 rows where experiment.platform = "ILLUMINA", tissue_curation = "Lateral Line" and tissue_curation_coarse = "Sensory System"
This data as json, CSV (advanced)
| Link | rowid ▼ | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
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| 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 | |||||||||||||||||||
| 56093 | 56093 | SRR10887617 | SRX7556598 | SRS5993979 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TGCGGC: hair cells wt 4H11 | GSM4271797 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TGCGGC: hair cells wt 4H11 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271797 | GSM4271797: TGCGGC: hair cells wt 4H11; Danio rerio; RNA Seq | GSM4271797 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271797 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TGCGGC_r1.fq.gz GEO_TGCGGC_r2.fq.gz | fastq fastq | 43663620.0 | 661570.0 | GSM4271797 r1 | 0:16 1:50 | A:10980262;C:9600102;G:10988621;T:12083118;N:11517 | 16 | 50 | 10980262 | 9600102 | 10988621 | 12083118 | 11517 | SRX7556598 | SRS5993979 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.89859 | 0.0 | 0.07802 | 1.0 | 0.97682 | 0.4968 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56094 | 56094 | SRR10887616 | SRX7556597 | SRS5993978 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TCGGCG: hair cells wt 4H10 | GSM4271796 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TCGGCG: hair cells wt 4H10 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271796 | GSM4271796: TCGGCG: hair cells wt 4H10; Danio rerio; RNA Seq | GSM4271796 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271796 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TCGGCG_r1.fq.gz GEO_TCGGCG_r2.fq.gz | fastq fastq | 22768350.0 | 344975.0 | GSM4271796 r1 | 0:16 1:50 | A:5596078;C:4886377;G:5930717;T:6350111;N:5067 | 16 | 50 | 5596078 | 4886377 | 5930717 | 6350111 | 5067 | SRX7556597 | SRS5993978 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.88535 | 0.0 | 0.08707 | 1.0 | 0.98494 | 0.4351 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56095 | 56095 | SRR10887615 | SRX7556596 | SRS5993982 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TCCCCG: hair cells wt 4H9 | GSM4271795 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TCCCCG: hair cells wt 4H9 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271795 | GSM4271795: TCCCCG: hair cells wt 4H9; Danio rerio; RNA Seq | GSM4271795 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271795 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TCCCCG_r1.fq.gz GEO_TCCCCG_r2.fq.gz | fastq fastq | 38242578.0 | 579433.0 | GSM4271795 r1 | 0:16 1:50 | A:9595312;C:9433451;G:8997891;T:10207672;N:8252 | 16 | 50 | 9595312 | 9433451 | 8997891 | 10207672 | 8252 | SRX7556596 | SRS5993982 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.81703 | 0.0 | 0.06164 | 1.0 | 0.97768 | 0.49143 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56096 | 56096 | SRR10887614 | SRX7556595 | SRS5993977 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GTCGGC: hair cells wt 4H8 | GSM4271794 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GTCGGC: hair cells wt 4H8 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271794 | GSM4271794: GTCGGC: hair cells wt 4H8; Danio rerio; RNA Seq | GSM4271794 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271794 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GTCGGC_r2.fq.gz GEO_GTCGGC_r1.fq.gz | fastq fastq | 24562824.0 | 372164.0 | GSM4271794 r1 | 0:16 1:50 | A:6106780;C:5478045;G:6286868;T:6684497;N:6634 | 16 | 50 | 6106780 | 5478045 | 6286868 | 6684497 | 6634 | SRX7556595 | SRS5993977 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.86176 | 0.0 | 0.07352 | 1.0 | 0.98052 | 0.45168 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56097 | 56097 | SRR10887613 | SRX7556594 | SRS5993976 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GGTGCG: hair cells wt 4H7 | GSM4271793 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GGTGCG: hair cells wt 4H7 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271793 | GSM4271793: GGTGCG: hair cells wt 4H7; Danio rerio; RNA Seq | GSM4271793 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271793 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GGTGCG_r1.fq.gz GEO_GGTGCG_r2.fq.gz | fastq fastq | 24573120.0 | 372320.0 | GSM4271793 r1 | 0:16 1:50 | A:6100442;C:5201156;G:6470564;T:6794081;N:6877 | 16 | 50 | 6100442 | 5201156 | 6470564 | 6794081 | 6877 | SRX7556594 | SRS5993976 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.84609 | 0.0 | 0.07426 | 1.0 | 0.98549 | 0.38014 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56098 | 56098 | SRR10887612 | SRX7556593 | SRS5993981 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GCGGGA: hair cells wt 4G11 | GSM4271792 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GCGGGA: hair cells wt 4G11 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271792 | GSM4271792: GCGGGA: hair cells wt 4G11; Danio rerio; RNA Seq | GSM4271792 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271792 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GCGGGA_r1.fq.gz GEO_GCGGGA_r2.fq.gz | fastq fastq | 27407886.0 | 415271.0 | GSM4271792 r1 | 0:16 1:50 | A:7308875;C:5649646;G:7245666;T:7196334;N:7365 | 16 | 50 | 7308875 | 5649646 | 7245666 | 7196334 | 7365 | SRX7556593 | SRS5993981 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.86238 | 0.0 | 0.07458 | 1.0 | 0.98571 | 0.47913 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56099 | 56099 | SRR10887611 | SRX7556592 | SRS5993974 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GCGCGT: hair cells wt 4G10 | GSM4271791 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GCGCGT: hair cells wt 4G10 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271791 | GSM4271791: GCGCGT: hair cells wt 4G10; Danio rerio; RNA Seq | GSM4271791 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271791 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GCGCGT_r1.fq.gz GEO_GCGCGT_r2.fq.gz | fastq fastq | 20750466.0 | 314401.0 | GSM4271791 r1 | 0:16 1:50 | A:5141353;C:4540611;G:5281606;T:5781160;N:5736 | 16 | 50 | 5141353 | 4540611 | 5281606 | 5781160 | 5736 | SRX7556592 | SRS5993974 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.88471 | 0.0 | 0.07169 | 1.0 | 0.98707 | 0.42399 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56100 | 56100 | SRR10887610 | SRX7556591 | SRS5993973 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GCGACG: hair cells wt 4G9 | GSM4271790 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GCGACG: hair cells wt 4G9 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271790 | GSM4271790: GCGACG: hair cells wt 4G9; Danio rerio; RNA Seq | GSM4271790 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271790 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GCGACG_r1.fq.gz GEO_GCGACG_r2.fq.gz | fastq fastq | 19658100.0 | 297850.0 | GSM4271790 r1 | 0:16 1:50 | A:5205744;C:4275466;G:5026996;T:5144761;N:5133 | 16 | 50 | 5205744 | 4275466 | 5026996 | 5144761 | 5133 | SRX7556591 | SRS5993973 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.89191 | 0.0 | 0.06686 | 1.0 | 0.98131 | 0.54948 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56101 | 56101 | SRR10887609 | SRX7556590 | SRS5993975 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GCCGGT: hair cells wt 4G8 | GSM4271789 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GCCGGT: hair cells wt 4G8 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271789 | GSM4271789: GCCGGT: hair cells wt 4G8; Danio rerio; RNA Seq | GSM4271789 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271789 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GCCGGT_r1.fq.gz GEO_GCCGGT_r2.fq.gz | fastq fastq | 34655676.0 | 525086.0 | GSM4271789 r1 | 0:16 1:50 | A:8563248;C:7767967;G:8892276;T:9422886;N:9299 | 16 | 50 | 8563248 | 7767967 | 8892276 | 9422886 | 9299 | SRX7556590 | SRS5993975 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.85312 | 0.0 | 0.06695 | 1.0 | 0.98524 | 0.39088 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56102 | 56102 | SRR10887608 | SRX7556589 | SRS5993980 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GCCCGA: hair cells wt 4G7 | GSM4271788 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GCCCGA: hair cells wt 4G7 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271788 | GSM4271788: GCCCGA: hair cells wt 4G7; Danio rerio; RNA Seq | GSM4271788 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271788 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GCCCGA_r1.fq.gz GEO_GCCCGA_r2.fq.gz | fastq fastq | 47296194.0 | 716609.0 | GSM4271788 r1 | 0:16 1:50 | A:12506634;C:11308000;G:11147016;T:12323583;N:10961 | 16 | 50 | 12506634 | 11308000 | 11147016 | 12323583 | 10961 | SRX7556589 | SRS5993980 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.75974 | 0.0 | 0.07461 | 1.0 | 0.98143 | 0.44424 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56103 | 56103 | SRR10887607 | SRX7556588 | SRS5993972 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CGGTCC: hair cells wt 4F12 | GSM4271787 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CGGTCC: hair cells wt 4F12 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271787 | GSM4271787: CGGTCC: hair cells wt 4F12; Danio rerio; RNA Seq | GSM4271787 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271787 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CGGTCC_r1.fq.gz GEO_CGGTCC_r2.fq.gz | fastq fastq | 25047000.0 | 379500.0 | GSM4271787 r1 | 0:16 1:50 | A:5998231;C:6033916;G:6166856;T:6841133;N:6864 | 16 | 50 | 5998231 | 6033916 | 6166856 | 6841133 | 6864 | SRX7556588 | SRS5993972 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.86579 | 0.0 | 0.06304 | 1.0 | 0.98557 | 0.40593 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56104 | 56104 | SRR10887606 | SRX7556587 | SRS5993971 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CGGGAG: hair cells wt 4F11 | GSM4271786 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CGGGAG: hair cells wt 4F11 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271786 | GSM4271786: CGGGAG: hair cells wt 4F11; Danio rerio; RNA Seq | GSM4271786 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271786 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CGGGAG_r1.fq.gz GEO_CGGGAG_r2.fq.gz | fastq fastq | 17233986.0 | 261121.0 | GSM4271786 r1 | 0:16 1:50 | A:4479383;C:3511799;G:4707128;T:4530531;N:5145 | 16 | 50 | 4479383 | 3511799 | 4707128 | 4530531 | 5145 | SRX7556587 | SRS5993971 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.89442 | 0.0 | 0.07953 | 1.0 | 0.98524 | 0.47235 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56105 | 56105 | SRR10887605 | SRX7556586 | SRS5993987 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CGGCAC: hair cells wt 4F10 | GSM4271785 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CGGCAC: hair cells wt 4F10 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271785 | GSM4271785: CGGCAC: hair cells wt 4F10; Danio rerio; RNA Seq | GSM4271785 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271785 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CGGCAC_r1.fq.gz GEO_CGGCAC_r2.fq.gz | fastq fastq | 30505200.0 | 462200.0 | GSM4271785 r1 | 0:16 1:50 | A:8102580;C:6867077;G:7305104;T:8221444;N:8995 | 16 | 50 | 8102580 | 6867077 | 7305104 | 8221444 | 8995 | SRX7556586 | SRS5993987 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.89338 | 0.0 | 0.08357 | 1.0 | 0.98557 | 0.50949 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56106 | 56106 | SRR10887604 | SRX7556585 | SRS5993968 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CGCTCG: hair cells wt 4F9 | GSM4271784 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CGCTCG: hair cells wt 4F9 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271784 | GSM4271784: CGCTCG: hair cells wt 4F9; Danio rerio; RNA Seq | GSM4271784 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271784 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CGCTCG_r2.fq.gz GEO_CGCTCG_r1.fq.gz | fastq fastq | 52351398.0 | 793203.0 | GSM4271784 r1 | 0:16 1:50 | A:12807706;C:12020314;G:13385072;T:14123256;N:15050 | 16 | 50 | 12807706 | 12020314 | 13385072 | 14123256 | 15050 | SRX7556585 | SRS5993968 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.57439 | 0.0 | 0.06392 | 1.0 | 0.98253 | 0.42209 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56107 | 56107 | SRR10887603 | SRX7556584 | SRS5993969 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CGCGAC: hair cells wt 4F8 | GSM4271783 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CGCGAC: hair cells wt 4F8 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271783 | GSM4271783: CGCGAC: hair cells wt 4F8; Danio rerio; RNA Seq | GSM4271783 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271783 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CGCGAC_r1.fq.gz GEO_CGCGAC_r2.fq.gz | fastq fastq | 23345586.0 | 353721.0 | GSM4271783 r1 | 0:16 1:50 | A:6171925;C:5383523;G:5555672;T:6227469;N:6997 | 16 | 50 | 6171925 | 5383523 | 5555672 | 6227469 | 6997 | SRX7556584 | SRS5993969 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.8601 | 0.0 | 0.10116 | 1.0 | 0.98419 | 0.4521 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56108 | 56108 | SRR10887602 | SRX7556583 | SRS5993967 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CGCCAG: hair cells wt 4F7 | GSM4271782 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CGCCAG: hair cells wt 4F7 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271782 | GSM4271782: CGCCAG: hair cells wt 4F7; Danio rerio; RNA Seq | GSM4271782 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271782 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CGCCAG_r1.fq.gz GEO_CGCCAG_r2.fq.gz | fastq fastq | 14317578.0 | 216933.0 | GSM4271782 r1 | 0:16 1:50 | A:3909348;C:3253582;G:3411025;T:3739224;N:4399 | 16 | 50 | 3909348 | 3253582 | 3411025 | 3739224 | 4399 | SRX7556583 | SRS5993967 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.79255 | 0.0 | 0.14794 | 1.0 | 0.98644 | 0.60725 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56109 | 56109 | SRR10887601 | SRX7556582 | SRS5993986 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CCAGGG: hair cells wt 4E12 | GSM4271781 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CCAGGG: hair cells wt 4E12 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271781 | GSM4271781: CCAGGG: hair cells wt 4E12; Danio rerio; RNA Seq | GSM4271781 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271781 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CCAGGG_r1.fq.gz GEO_CCAGGG_r2.fq.gz | fastq fastq | 24273084.0 | 367774.0 | GSM4271781 r1 | 0:16 1:50 | A:6469335;C:5140316;G:6075899;T:6580531;N:7003 | 16 | 50 | 6469335 | 5140316 | 6075899 | 6580531 | 7003 | SRX7556582 | SRS5993986 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.86792 | 0.0 | 0.13118 | 1.0 | 0.98466 | 0.51743 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56110 | 56110 | SRR10887600 | SRX7556581 | SRS5993966 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CAGGCC: hair cells wt 4E11 | GSM4271780 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CAGGCC: hair cells wt 4E11 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271780 | GSM4271780: CAGGCC: hair cells wt 4E11; Danio rerio; RNA Seq | GSM4271780 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271780 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CAGGCC_r2.fq.gz GEO_CAGGCC_r1.fq.gz | fastq fastq | 21957210.0 | 332685.0 | GSM4271780 r1 | 0:16 1:50 | A:5733552;C:5210288;G:5238165;T:5768948;N:6257 | 16 | 50 | 5733552 | 5210288 | 5238165 | 5768948 | 6257 | SRX7556581 | SRS5993966 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.82741 | 0.0 | 0.0895 | 1.0 | 0.9862 | 0.50397 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56111 | 56111 | SRR10887599 | SRX7556580 | SRS5993970 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CACGCG: hair cells wt 4E10 | GSM4271779 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CACGCG: hair cells wt 4E10 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271779 | GSM4271779: CACGCG: hair cells wt 4E10; Danio rerio; RNA Seq | GSM4271779 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271779 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CACGCG_r1.fq.gz GEO_CACGCG_r2.fq.gz | fastq fastq | 25959582.0 | 393327.0 | GSM4271779 r1 | 0:16 1:50 | A:6981800;C:5837017;G:6108203;T:7025734;N:6828 | 16 | 50 | 6981800 | 5837017 | 6108203 | 7025734 | 6828 | SRX7556580 | SRS5993970 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.86201 | 0.0 | 0.10766 | 1.0 | 0.98464 | 0.46435 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56112 | 56112 | SRR10887598 | SRX7556579 | SRS5993965 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | AGGGCG: hair cells wt 4E9 | GSM4271778 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | AGGGCG: hair cells wt 4E9 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271778 | GSM4271778: AGGGCG: hair cells wt 4E9; Danio rerio; RNA Seq | GSM4271778 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271778 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_AGGGCG_r1.fq.gz GEO_AGGGCG_r2.fq.gz | fastq fastq | 22538274.0 | 341489.0 | GSM4271778 r1 | 0:16 1:50 | A:6077196;C:4338921;G:5951815;T:6165292;N:5050 | 16 | 50 | 6077196 | 4338921 | 5951815 | 6165292 | 5050 | SRX7556579 | SRS5993965 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.8557 | 0.0 | 0.1692 | 1.0 | 0.98042 | 0.55115 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56113 | 56113 | SRR10887597 | SRX7556578 | SRS5993984 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | AGCGCC: hair cells wt 4E8 | GSM4271777 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | AGCGCC: hair cells wt 4E8 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271777 | GSM4271777: AGCGCC: hair cells wt 4E8; Danio rerio; RNA Seq | GSM4271777 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271777 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_AGCGCC_r1.fq.gz GEO_AGCGCC_r2.fq.gz | fastq fastq | 16579134.0 | 251199.0 | GSM4271777 r1 | 0:16 1:50 | A:4407189;C:3879034;G:3989040;T:4299921;N:3950 | 16 | 50 | 4407189 | 3879034 | 3989040 | 4299921 | 3950 | SRX7556578 | SRS5993984 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.81806 | 0.0 | 0.06974 | 1.0 | 0.9847 | 0.47148 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56114 | 56114 | SRR10887596 | SRX7556577 | SRS5993985 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | ACGGCC: hair cells wt 4E7 | GSM4271776 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | ACGGCC: hair cells wt 4E7 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271776 | GSM4271776: ACGGCC: hair cells wt 4E7; Danio rerio; RNA Seq | GSM4271776 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271776 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_ACGGCC_r1.fq.gz GEO_ACGGCC_r2.fq.gz | fastq fastq | 118857420.0 | 1800870.0 | GSM4271776 r1 | 0:16 1:50 | A:29791771;C:29519453;G:31033819;T:28481312;N:31065 | 16 | 50 | 29791771 | 29519453 | 31033819 | 28481312 | 31065 | SRX7556577 | SRS5993985 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.72883 | 0.0 | 0.23389 | 1.0 | 0.97792 | 0.5079 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56115 | 56115 | SRR10887595 | SRX7556576 | SRS5993962 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GATCGT: hair cells wt 4D12 | GSM4271775 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GATCGT: hair cells wt 4D12 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271775 | GSM4271775: GATCGT: hair cells wt 4D12; Danio rerio; RNA Seq | GSM4271775 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271775 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GATCGT_r1.fq.gz GEO_GATCGT_r2.fq.gz | fastq fastq | 33894102.0 | 513547.0 | GSM4271775 r1 | 0:16 1:50 | A:8954709;C:6672608;G:8290536;T:9966379;N:9870 | 16 | 50 | 8954709 | 6672608 | 8290536 | 9966379 | 9870 | SRX7556576 | SRS5993962 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.88831 | 0.0 | 0.07983 | 1.0 | 0.98029 | 0.48458 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56116 | 56116 | SRR10887594 | SRX7556575 | SRS5993964 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CGATTG: hair cells wt 4D11 | GSM4271774 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CGATTG: hair cells wt 4D11 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271774 | GSM4271774: CGATTG: hair cells wt 4D11; Danio rerio; RNA Seq | GSM4271774 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271774 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CGATTG_r1.fq.gz GEO_CGATTG_r2.fq.gz | fastq fastq | 18082020.0 | 273970.0 | GSM4271774 r1 | 0:16 1:50 | A:4869073;C:3585379;G:4430790;T:5191055;N:5723 | 16 | 50 | 4869073 | 3585379 | 4430790 | 5191055 | 5723 | SRX7556575 | SRS5993964 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.84709 | 0.0 | 0.19188 | 1.0 | 0.98086 | 0.52053 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56117 | 56117 | SRR10887593 | SRX7556574 | SRS5993960 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CATGGT: hair cells wt 4D10 | GSM4271773 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CATGGT: hair cells wt 4D10 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271773 | GSM4271773: CATGGT: hair cells wt 4D10; Danio rerio; RNA Seq | GSM4271773 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271773 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CATGGT_r1.fq.gz GEO_CATGGT_r2.fq.gz | fastq fastq | 22401654.0 | 339419.0 | GSM4271773 r1 | 0:16 1:50 | A:5861732;C:4558444;G:5514064;T:6461033;N:6381 | 16 | 50 | 5861732 | 4558444 | 5514064 | 6461033 | 6381 | SRX7556574 | SRS5993960 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.85022 | 0.0 | 0.07553 | 1.0 | 0.98433 | 0.43146 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56118 | 56118 | SRR10887592 | SRX7556573 | SRS5993961 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CAAGCT: hair cells wt 4D9 | GSM4271772 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CAAGCT: hair cells wt 4D9 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271772 | GSM4271772: CAAGCT: hair cells wt 4D9; Danio rerio; RNA Seq | GSM4271772 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271772 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CAAGCT_r1.fq.gz GEO_CAAGCT_r2.fq.gz | fastq fastq | 21428154.0 | 324669.0 | GSM4271772 r1 | 0:16 1:50 | A:5942829;C:4731188;G:4990655;T:5756895;N:6587 | 16 | 50 | 5942829 | 4731188 | 4990655 | 5756895 | 6587 | SRX7556573 | SRS5993961 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.84948 | 0.0 | 0.11697 | 1.0 | 0.98482 | 0.49134 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56119 | 56119 | SRR10887591 | SRX7556572 | SRS5993958 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | ACCGTA: hair cells wt 4D8 | GSM4271771 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | ACCGTA: hair cells wt 4D8 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271771 | GSM4271771: ACCGTA: hair cells wt 4D8; Danio rerio; RNA Seq | GSM4271771 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271771 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_ACCGTA_r1.fq.gz GEO_ACCGTA_r2.fq.gz | fastq fastq | 32023728.0 | 485208.0 | GSM4271771 r1 | 0:16 1:50 | A:8851322;C:7094664;G:7465921;T:8602598;N:9223 | 16 | 50 | 8851322 | 7094664 | 7465921 | 8602598 | 9223 | SRX7556572 | SRS5993958 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.81584 | 0.0 | 0.07569 | 1.0 | 0.98701 | 0.43154 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56120 | 56120 | SRR10887590 | SRX7556571 | SRS5993957 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TTTTCT: hair cells wt 4D7 | GSM4271770 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TTTTCT: hair cells wt 4D7 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271770 | GSM4271770: TTTTCT: hair cells wt 4D7; Danio rerio; RNA Seq | GSM4271770 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271770 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TTTTCT_r1.fq.gz GEO_TTTTCT_r2.fq.gz | fastq fastq | 30970962.0 | 469257.0 | GSM4271770 r1 | 0:16 1:50 | A:7685607;C:6225340;G:6659308;T:10392742;N:7965 | 16 | 50 | 7685607 | 6225340 | 6659308 | 10392742 | 7965 | SRX7556571 | SRS5993957 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.83325 | 0.0 | 0.10718 | 1.0 | 0.98157 | 0.49058 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56121 | 56121 | SRR10887589 | SRX7556570 | SRS5993955 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TGTTAT: hair cells wt 4C12 | GSM4271769 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TGTTAT: hair cells wt 4C12 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271769 | GSM4271769: TGTTAT: hair cells wt 4C12; Danio rerio; RNA Seq | GSM4271769 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271769 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TGTTAT_r1.fq.gz GEO_TGTTAT_r2.fq.gz | fastq fastq | 27958458.0 | 423613.0 | GSM4271769 r1 | 0:16 1:50 | A:7253350;C:5460413;G:6559816;T:8677521;N:7358 | 16 | 50 | 7253350 | 5460413 | 6559816 | 8677521 | 7358 | SRX7556570 | SRS5993955 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.83012 | 0.0 | 0.08904 | 1.0 | 0.98675 | 0.37785 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Multi-stage | Multi-stage | Lateral Line | Sensory System | |||||||||||
| 56122 | 56122 | SRR10887588 | SRX7556569 | SRS5993963 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TGATAA: hair cells wt 4C11 | GSM4271768 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TGATAA: hair cells wt 4C11 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271768 | GSM4271768: TGATAA: hair cells wt 4C11; Danio rerio; RNA Seq | GSM4271768 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271768 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TGATAA_r1.fq.gz GEO_TGATAA_r2.fq.gz | fastq fastq | 16311570.0 | 247145.0 | GSM4271768 r1 | 0:16 1:50 | A:4698682;C:3073287;G:3789253;T:4746028;N:4320 | 16 | 50 | 4698682 | 3073287 | 3789253 | 4746028 | 4320 | SRX7556569 | SRS5993963 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.83888 | 0.0 | 0.09183 | 1.0 | 0.98715 | 0.45564 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Multi-stage | Multi-stage | Lateral Line | Sensory System | |||||||||||
| 56123 | 56123 | SRR10887587 | SRX7556568 | SRS5993959 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TCTATA: hair cells wt 4C10 | GSM4271767 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TCTATA: hair cells wt 4C10 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271767 | GSM4271767: TCTATA: hair cells wt 4C10; Danio rerio; RNA Seq | GSM4271767 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271767 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TCTATA_r1.fq.gz GEO_TCTATA_r2.fq.gz | fastq fastq | 21750102.0 | 329547.0 | GSM4271767 r1 | 0:16 1:50 | A:6098788;C:4298102;G:4613696;T:6733786;N:5730 | 16 | 50 | 6098788 | 4298102 | 4613696 | 6733786 | 5730 | SRX7556568 | SRS5993959 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.88556 | 0.0 | 0.09247 | 1.0 | 0.98632 | 0.51526 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Multi-stage | Multi-stage | Lateral Line | Sensory System | |||||||||||
| 56124 | 56124 | SRR10887586 | SRX7556567 | SRS5993954 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TCAATT: hair cells wt 4C9 | GSM4271766 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TCAATT: hair cells wt 4C9 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271766 | GSM4271766: TCAATT: hair cells wt 4C9; Danio rerio; RNA Seq | GSM4271766 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271766 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TCAATT_r1.fq.gz GEO_TCAATT_r2.fq.gz | fastq fastq | 23862894.0 | 361559.0 | GSM4271766 r1 | 0:16 1:50 | A:6588667;C:4897780;G:5179183;T:7191284;N:5980 | 16 | 50 | 6588667 | 4897780 | 5179183 | 7191284 | 5980 | SRX7556567 | SRS5993954 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.86481 | 0.0 | 0.11034 | 1.0 | 0.98326 | 0.40522 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Multi-stage | Multi-stage | Lateral Line | Sensory System | |||||||||||
| 56125 | 56125 | SRR10887585 | SRX7556566 | SRS5993956 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TATTCA: hair cells wt 4C8 | GSM4271765 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TATTCA: hair cells wt 4C8 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271765 | GSM4271765: TATTCA: hair cells wt 4C8; Danio rerio; RNA Seq | GSM4271765 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271765 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TATTCA_r1.fq.gz GEO_TATTCA_r2.fq.gz | fastq fastq | 17886990.0 | 271015.0 | GSM4271765 r1 | 0:16 1:50 | A:4891618;C:3686776;G:3988141;T:5315845;N:4610 | 16 | 50 | 4891618 | 3686776 | 3988141 | 5315845 | 4610 | SRX7556566 | SRS5993956 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.81672 | 0.0 | 0.1005 | 1.0 | 0.98561 | 0.42678 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Multi-stage | Multi-stage | Lateral Line | Sensory System | |||||||||||
| 56126 | 56126 | SRR10887584 | SRX7556565 | SRS5993952 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TATCTA: hair cells wt 4C7 | GSM4271764 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TATCTA: hair cells wt 4C7 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271764 | GSM4271764: TATCTA: hair cells wt 4C7; Danio rerio; RNA Seq | GSM4271764 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271764 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TATCTA_r1.fq.gz GEO_TATCTA_r2.fq.gz | fastq fastq | 67991880.0 | 1030180.0 | GSM4271764 r1 | 0:16 1:50 | A:18256048;C:14118538;G:16365381;T:19234623;N:17290 | 16 | 50 | 18256048 | 14118538 | 16365381 | 19234623 | 17290 | SRX7556565 | SRS5993952 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.74612 | 0.0 | 0.10089 | 1.0 | 0.97877 | 0.49534 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Multi-stage | Multi-stage | Lateral Line | Sensory System | |||||||||||
| 56127 | 56127 | SRR10887583 | SRX7556564 | SRS5993953 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GTTATT: hair cells wt 4B12 | GSM4271763 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GTTATT: hair cells wt 4B12 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271763 | GSM4271763: GTTATT: hair cells wt 4B12; Danio rerio; RNA Seq | GSM4271763 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271763 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GTTATT_r1.fq.gz GEO_GTTATT_r2.fq.gz | fastq fastq | 33621720.0 | 509420.0 | GSM4271763 r1 | 0:16 1:50 | A:8782917;C:6333781;G:7803342;T:10694526;N:7154 | 16 | 50 | 8782917 | 6333781 | 7803342 | 10694526 | 7154 | SRX7556564 | SRS5993953 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.83277 | 0.0 | 0.09046 | 1.0 | 0.98208 | 0.42767 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56128 | 56128 | SRR10887582 | SRX7556563 | SRS5993950 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GTAAAT: hair cells wt 4B11 | GSM4271762 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GTAAAT: hair cells wt 4B11 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271762 | GSM4271762: GTAAAT: hair cells wt 4B11; Danio rerio; RNA Seq | GSM4271762 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271762 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GTAAAT_r1.fq.gz GEO_GTAAAT_r2.fq.gz | fastq fastq | 32995116.0 | 499926.0 | GSM4271762 r1 | 0:16 1:50 | A:9697104;C:6185335;G:7695283;T:9409420;N:7974 | 16 | 50 | 9697104 | 6185335 | 7695283 | 9409420 | 7974 | SRX7556563 | SRS5993950 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.86836 | 0.0 | 0.1074 | 1.0 | 0.98384 | 0.42561 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56129 | 56129 | SRR10887581 | SRX7556562 | SRS5993949 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GAATTA: hair cells wt 4B10 | GSM4271761 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GAATTA: hair cells wt 4B10 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271761 | GSM4271761: GAATTA: hair cells wt 4B10; Danio rerio; RNA Seq | GSM4271761 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271761 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GAATTA_r1.fq.gz GEO_GAATTA_r2.fq.gz | fastq fastq | 33700524.0 | 510614.0 | GSM4271761 r1 | 0:16 1:50 | A:9951851;C:6205852;G:7868259;T:9667023;N:7539 | 16 | 50 | 9951851 | 6205852 | 7868259 | 9667023 | 7539 | SRX7556562 | SRS5993949 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.86693 | 0.0 | 0.08211 | 1.0 | 0.9807 | 0.4477 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56130 | 56130 | SRR10887580 | SRX7556561 | SRS5993951 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CTTATA: hair cells wt 4B9 | GSM4271760 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CTTATA: hair cells wt 4B9 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271760 | GSM4271760: CTTATA: hair cells wt 4B9; Danio rerio; RNA Seq | GSM4271760 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271760 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CTTATA_r2.fq.gz GEO_CTTATA_r1.fq.gz | fastq fastq | 18144654.0 | 274919.0 | GSM4271760 r1 | 0:16 1:50 | A:5154253;C:3585215;G:3991271;T:5409596;N:4319 | 16 | 50 | 5154253 | 3585215 | 3991271 | 5409596 | 4319 | SRX7556561 | SRS5993951 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.81083 | 0.0 | 0.12691 | 1.0 | 0.97979 | 0.53705 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56131 | 56131 | SRR10887579 | SRX7556560 | SRS5993947 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CTAATT: hair cells wt 4B8 | GSM4271759 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CTAATT: hair cells wt 4B8 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271759 | GSM4271759: CTAATT: hair cells wt 4B8; Danio rerio; RNA Seq | GSM4271759 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271759 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CTAATT_r1.fq.gz GEO_CTAATT_r2.fq.gz | fastq fastq | 21875304.0 | 331444.0 | GSM4271759 r1 | 0:16 1:50 | A:6178378;C:4411583;G:4735412;T:6545030;N:4901 | 16 | 50 | 6178378 | 4411583 | 4735412 | 6545030 | 4901 | SRX7556560 | SRS5993947 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.79469 | 0.0 | 0.15397 | 1.0 | 0.9847 | 0.52729 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56132 | 56132 | SRR10887578 | SRX7556559 | SRS5993946 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CATATT: hair cells wt 4B7 | GSM4271758 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CATATT: hair cells wt 4B7 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271758 | GSM4271758: CATATT: hair cells wt 4B7; Danio rerio; RNA Seq | GSM4271758 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271758 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CATATT_r1.fq.gz GEO_CATATT_r2.fq.gz | fastq fastq | 2295744.0 | 34784.0 | GSM4271758 r1 | 0:16 1:50 | A:639356;C:454332;G:505930;T:695524;N:602 | 16 | 50 | 639356 | 454332 | 505930 | 695524 | 602 | SRX7556559 | SRS5993946 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.75545 | 0.0 | 0.11978 | 1.0 | 0.99239 | 0.47601 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56133 | 56133 | SRR10887577 | SRX7556558 | SRS5993945 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | ATAGTA: hair cells wt 4A12 | GSM4271757 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | ATAGTA: hair cells wt 4A12 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271757 | GSM4271757: ATAGTA: hair cells wt 4A12; Danio rerio; RNA Seq | GSM4271757 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271757 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_ATAGTA_r1.fq.gz GEO_ATAGTA_r2.fq.gz | fastq fastq | 29857542.0 | 452387.0 | GSM4271757 r1 | 0:16 1:50 | A:8650587;C:5671216;G:6756185;T:8771447;N:8107 | 16 | 50 | 8650587 | 5671216 | 6756185 | 8771447 | 8107 | SRX7556558 | SRS5993945 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.8678 | 0.0 | 0.0651 | 1.0 | 0.98502 | 0.43445 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56134 | 56134 | SRR10887576 | SRX7556557 | SRS5993943 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | ATAATG: hair cells wt 4A11 | GSM4271756 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | ATAATG: hair cells wt 4A11 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271756 | GSM4271756: ATAATG: hair cells wt 4A11; Danio rerio; RNA Seq | GSM4271756 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271756 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_ATAATG_r2.fq.gz GEO_ATAATG_r1.fq.gz | fastq fastq | 4178658.0 | 63313.0 | GSM4271756 r1 | 0:16 1:50 | A:1254421;C:788868;G:971659;T:1162609;N:1101 | 16 | 50 | 1254421 | 788868 | 971659 | 1162609 | 1101 | SRX7556557 | SRS5993943 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.70686 | 0.0 | 0.57365 | 1.0 | 0.99066 | 0.50095 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56135 | 56135 | SRR10887575 | SRX7556556 | SRS5993942 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | AGTTAA: hair cells wt 4A10 | GSM4271755 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | AGTTAA: hair cells wt 4A10 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271755 | GSM4271755: AGTTAA: hair cells wt 4A10; Danio rerio; RNA Seq | GSM4271755 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271755 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_AGTTAA_r1.fq.gz GEO_AGTTAA_r2.fq.gz | fastq fastq | 34809588.0 | 527418.0 | GSM4271755 r1 | 0:16 1:50 | A:10137071;C:6623358;G:8098271;T:9941324;N:9564 | 16 | 50 | 10137071 | 6623358 | 8098271 | 9941324 | 9564 | SRX7556556 | SRS5993942 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.8522 | 0.0 | 0.06792 | 1.0 | 0.98577 | 0.39584 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56136 | 56136 | SRR10887574 | SRX7556555 | SRS5993948 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | AGATAT: hair cells wt 4A9 | GSM4271754 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | AGATAT: hair cells wt 4A9 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271754 | GSM4271754: AGATAT: hair cells wt 4A9; Danio rerio; RNA Seq | GSM4271754 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271754 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_AGATAT_r2.fq.gz GEO_AGATAT_r1.fq.gz | fastq fastq | 28077060.0 | 425410.0 | GSM4271754 r1 | 0:16 1:50 | A:8318473;C:5276710;G:6472058;T:8001915;N:7904 | 16 | 50 | 8318473 | 5276710 | 6472058 | 8001915 | 7904 | SRX7556555 | SRS5993948 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.86296 | 0.0 | 0.09442 | 1.0 | 0.98157 | 0.41782 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56137 | 56137 | SRR10887573 | SRX7556554 | SRS5993941 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | ACTATT: hair cells wt 4A8 | GSM4271753 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | ACTATT: hair cells wt 4A8 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271753 | GSM4271753: ACTATT: hair cells wt 4A8; Danio rerio; RNA Seq | GSM4271753 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271753 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_ACTATT_r1.fq.gz GEO_ACTATT_r2.fq.gz | fastq fastq | 36810312.0 | 557732.0 | GSM4271753 r1 | 0:16 1:50 | A:10070588;C:7531734;G:7811902;T:11387603;N:8485 | 16 | 50 | 10070588 | 7531734 | 7811902 | 11387603 | 8485 | SRX7556554 | SRS5993941 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.87534 | 0.0 | 0.07813 | 1.0 | 0.98384 | 0.46263 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56138 | 56138 | SRR10887572 | SRX7556553 | SRS5993944 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | ACAAAT: hair cells wt 4A7 | GSM4271752 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | ACAAAT: hair cells wt 4A7 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271752 | GSM4271752: ACAAAT: hair cells wt 4A7; Danio rerio; RNA Seq | GSM4271752 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271752 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_ACAAAT_r1.fq.gz GEO_ACAAAT_r2.fq.gz | fastq fastq | 75215184.0 | 1139624.0 | GSM4271752 r1 | 0:16 1:50 | A:22762180;C:15723998;G:17654105;T:19052173;N:22728 | 16 | 50 | 22762180 | 15723998 | 17654105 | 19052173 | 22728 | SRX7556553 | SRS5993944 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.69908 | 0.0 | 0.11765 | 1.0 | 0.97737 | 0.44964 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56139 | 56139 | SRR10887571 | SRX7556552 | SRS5993939 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TGCCCC: hair cells wt 2H11 | GSM4271751 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TGCCCC: hair cells wt 2H11 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271751 | GSM4271751: TGCCCC: hair cells wt 2H11; Danio rerio; RNA Seq | GSM4271751 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271751 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TGCCCC_r1.fq.gz GEO_TGCCCC_r2.fq.gz | fastq fastq | 99705870.0 | 1510695.0 | GSM4271751 r1 | 0:16 1:50 | A:24784931;C:24938972;G:23296385;T:26663615;N:21967 | 16 | 50 | 24784931 | 24938972 | 23296385 | 26663615 | 21967 | SRX7556552 | SRS5993939 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.80511 | 0.0 | 0.11382 | 1.0 | 0.96601 | 0.44049 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56140 | 56140 | SRR10887570 | SRX7556551 | SRS5993938 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TCCGGG: hair cells wt 2H10 | GSM4271750 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TCCGGG: hair cells wt 2H10 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271750 | GSM4271750: TCCGGG: hair cells wt 2H10; Danio rerio; RNA Seq | GSM4271750 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271750 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TCCGGG_r1.fq.gz GEO_TCCGGG_r2.fq.gz | fastq fastq | 156814680.0 | 2375980.0 | GSM4271750 r1 | 0:16 1:50 | A:36405105;C:36084740;G:45725833;T:38559969;N:39033 | 16 | 50 | 36405105 | 36084740 | 45725833 | 38559969 | 39033 | SRX7556551 | SRS5993938 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.64184 | 0.0 | 0.13248 | 1.0 | 0.97745 | 0.55947 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56141 | 56141 | SRR10887569 | SRX7556550 | SRS5993935 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GTGGCC: hair cells wt 2H9 | GSM4271749 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GTGGCC: hair cells wt 2H9 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271749 | GSM4271749: GTGGCC: hair cells wt 2H9; Danio rerio; RNA Seq | GSM4271749 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271749 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GTGGCC_r1.fq.gz GEO_GTGGCC_r2.fq.gz | fastq fastq | 10173966.0 | 154151.0 | GSM4271749 r1 | 0:16 1:50 | A:2501984;C:2250525;G:2956615;T:2462095;N:2747 | 16 | 50 | 2501984 | 2250525 | 2956615 | 2462095 | 2747 | SRX7556550 | SRS5993935 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.25254 | 0.0 | 0.11303 | 1.0 | 0.97701 | 0.51611 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56142 | 56142 | SRR10887568 | SRX7556549 | SRS5993940 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GTCCCC: hair cells wt 2H8 | GSM4271748 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GTCCCC: hair cells wt 2H8 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271748 | GSM4271748: GTCCCC: hair cells wt 2H8; Danio rerio; RNA Seq | GSM4271748 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271748 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GTCCCC_r1.fq.gz GEO_GTCCCC_r2.fq.gz | fastq fastq | 88909656.0 | 1347116.0 | GSM4271748 r1 | 0:16 1:50 | A:22744809;C:21441987;G:19271731;T:25429628;N:21501 | 16 | 50 | 22744809 | 21441987 | 19271731 | 25429628 | 21501 | SRX7556549 | SRS5993940 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.89945 | 0.0 | 0.54925 | 1.0 | 0.97522 | 0.51973 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56143 | 56143 | SRR10887567 | SRX7556548 | SRS5993936 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GGGTGC: hair cells wt 2H7 | GSM4271747 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GGGTGC: hair cells wt 2H7 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271747 | GSM4271747: GGGTGC: hair cells wt 2H7; Danio rerio; RNA Seq | GSM4271747 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271747 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GGGTGC_r1.fq.gz GEO_GGGTGC_r2.fq.gz | fastq fastq | 49002294.0 | 742459.0 | GSM4271747 r1 | 0:16 1:50 | A:11795313;C:10365939;G:14029826;T:12796902;N:14314 | 16 | 50 | 11795313 | 10365939 | 14029826 | 12796902 | 14314 | SRX7556548 | SRS5993936 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.7657 | 0.0 | 0.10651 | 1.0 | 0.98167 | 0.52497 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56144 | 56144 | SRR10887566 | SRX7556547 | SRS5993937 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GCGGAG: hair cells wt 2G11 | GSM4271746 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GCGGAG: hair cells wt 2G11 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271746 | GSM4271746: GCGGAG: hair cells wt 2G11; Danio rerio; RNA Seq | GSM4271746 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271746 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GCGGAG_r1.fq.gz GEO_GCGGAG_r2.fq.gz | fastq fastq | 61406334.0 | 930399.0 | GSM4271746 r1 | 0:16 1:50 | A:16036263;C:12621880;G:17084575;T:15647426;N:16190 | 16 | 50 | 16036263 | 12621880 | 17084575 | 15647426 | 16190 | SRX7556547 | SRS5993937 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.82866 | 0.0 | 0.08484 | 1.0 | 0.97928 | 0.44046 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56145 | 56145 | SRR10887565 | SRX7556546 | SRS5993934 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GCGCAC: hair cells wt 2G10 | GSM4271745 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GCGCAC: hair cells wt 2G10 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271745 | GSM4271745: GCGCAC: hair cells wt 2G10; Danio rerio; RNA Seq | GSM4271745 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271745 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GCGCAC_r1.fq.gz GEO_GCGCAC_r2.fq.gz | fastq fastq | 103715700.0 | 1571450.0 | GSM4271745 r1 | 0:16 1:50 | A:27215760;C:23945117;G:26070541;T:26455572;N:28710 | 16 | 50 | 27215760 | 23945117 | 26070541 | 26455572 | 28710 | SRX7556546 | SRS5993934 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.85772 | 0.0 | 0.1198 | 1.0 | 0.9791 | 0.48025 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56146 | 56146 | SRR10887564 | SRX7556545 | SRS5993930 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GCCTCG: hair cells wt 2G9 | GSM4271744 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GCCTCG: hair cells wt 2G9 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271744 | GSM4271744: GCCTCG: hair cells wt 2G9; Danio rerio; RNA Seq | GSM4271744 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271744 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GCCTCG_r1.fq.gz GEO_GCCTCG_r2.fq.gz | fastq fastq | 23640144.0 | 358184.0 | GSM4271744 r1 | 0:16 1:50 | A:5894883;C:5651176;G:5830213;T:6257556;N:6316 | 16 | 50 | 5894883 | 5651176 | 5830213 | 6257556 | 6316 | SRX7556545 | SRS5993930 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.77455 | 0.0 | 0.09583 | 1.0 | 0.98315 | 0.43472 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56147 | 56147 | SRR10887563 | SRX7556544 | SRS5993929 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GCCGAC: hair cells wt 2G8 | GSM4271743 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GCCGAC: hair cells wt 2G8 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271743 | GSM4271743: GCCGAC: hair cells wt 2G8; Danio rerio; RNA Seq | GSM4271743 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271743 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GCCGAC_r1.fq.gz GEO_GCCGAC_r2.fq.gz | fastq fastq | 38128794.0 | 577709.0 | GSM4271743 r1 | 0:16 1:50 | A:9934273;C:9007484;G:9673915;T:9495594;N:17528 | 16 | 50 | 9934273 | 9007484 | 9673915 | 9495594 | 17528 | SRX7556544 | SRS5993929 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.77242 | 0.0 | 0.0868 | 1.0 | 0.98506 | 0.44418 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56148 | 56148 | SRR10887562 | SRX7556543 | SRS5993932 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GCCCAG: hair cells wt 2G7 | GSM4271742 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GCCCAG: hair cells wt 2G7 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271742 | GSM4271742: GCCCAG: hair cells wt 2G7; Danio rerio; RNA Seq | GSM4271742 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271742 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GCCCAG_r1.fq.gz GEO_GCCCAG_r2.fq.gz | fastq fastq | 46788522.0 | 708917.0 | GSM4271742 r1 | 0:16 1:50 | A:12323933;C:10883758;G:11730463;T:11837342;N:13026 | 16 | 50 | 12323933 | 10883758 | 11730463 | 11837342 | 13026 | SRX7556543 | SRS5993932 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.77399 | 0.0 | 0.08918 | 1.0 | 0.98005 | 0.44547 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56149 | 56149 | SRR10887561 | SRX7556542 | SRS5993927 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CGGGGA: hair cells wt 2F12 | GSM4271741 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CGGGGA: hair cells wt 2F12 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271741 | GSM4271741: CGGGGA: hair cells wt 2F12; Danio rerio; RNA Seq | GSM4271741 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271741 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CGGGGA_r1.fq.gz GEO_CGGGGA_r2.fq.gz | fastq fastq | 29135040.0 | 441440.0 | GSM4271741 r1 | 0:16 1:50 | A:7693442;C:5930976;G:8161519;T:7339852;N:9251 | 16 | 50 | 7693442 | 5930976 | 8161519 | 7339852 | 9251 | SRX7556542 | SRS5993927 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.82074 | 0.0 | 0.11249 | 1.0 | 0.9763 | 0.41743 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56150 | 56150 | SRR10887560 | SRX7556541 | SRS5993926 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CGGCGT: hair cells wt 2F11 | GSM4271740 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CGGCGT: hair cells wt 2F11 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271740 | GSM4271740: CGGCGT: hair cells wt 2F11; Danio rerio; RNA Seq | GSM4271740 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271740 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CGGCGT_r1.fq.gz GEO_CGGCGT_r2.fq.gz | fastq fastq | 53204382.0 | 806127.0 | GSM4271740 r1 | 0:16 1:50 | A:13239467;C:11643256;G:14105165;T:14200599;N:15895 | 16 | 50 | 13239467 | 11643256 | 14105165 | 14200599 | 15895 | SRX7556541 | SRS5993926 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.78045 | 0.0 | 0.08602 | 1.0 | 0.98171 | 0.42093 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56151 | 56151 | SRR10887559 | SRX7556540 | SRS5993933 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CGGACG: hair cells wt 2F10 | GSM4271739 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CGGACG: hair cells wt 2F10 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271739 | GSM4271739: CGGACG: hair cells wt 2F10; Danio rerio; RNA Seq | GSM4271739 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271739 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CGGACG_r1.fq.gz GEO_CGGACG_r2.fq.gz | fastq fastq | 113671008.0 | 1722288.0 | GSM4271739 r1 | 0:16 1:50 | A:30256021;C:24026594;G:29758029;T:29596584;N:33780 | 16 | 50 | 30256021 | 24026594 | 29758029 | 29596584 | 33780 | SRX7556540 | SRS5993933 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.87614 | 0.0 | 0.14295 | 1.0 | 0.97688 | 0.48159 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56152 | 56152 | SRR10887558 | SRX7556539 | SRS5993928 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CGCGGT: hair cells wt 2F9 | GSM4271738 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CGCGGT: hair cells wt 2F9 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271738 | GSM4271738: CGCGGT: hair cells wt 2F9; Danio rerio; RNA Seq | GSM4271738 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271738 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CGCGGT_r1.fq.gz GEO_CGCGGT_r2.fq.gz | fastq fastq | 59444088.0 | 900668.0 | GSM4271738 r1 | 0:16 1:50 | A:14758639;C:12847168;G:15472154;T:16349050;N:17077 | 16 | 50 | 14758639 | 12847168 | 15472154 | 16349050 | 17077 | SRX7556539 | SRS5993928 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.85772 | 0.0 | 0.06994 | 1.0 | 0.98027 | 0.44563 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56153 | 56153 | SRR10887557 | SRX7556538 | SRS5993925 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CGCCGA: hair cells wt 2F8 | GSM4271737 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CGCCGA: hair cells wt 2F8 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271737 | GSM4271737: CGCCGA: hair cells wt 2F8; Danio rerio; RNA Seq | GSM4271737 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271737 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CGCCGA_r1.fq.gz GEO_CGCCGA_r2.fq.gz | fastq fastq | 58332450.0 | 883825.0 | GSM4271737 r1 | 0:16 1:50 | A:15100292;C:13840300;G:15452320;T:13923439;N:16099 | 16 | 50 | 15100292 | 13840300 | 15452320 | 13923439 | 16099 | SRX7556538 | SRS5993925 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.72198 | 0.0 | 0.09689 | 1.0 | 0.98119 | 0.42056 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56154 | 56154 | SRR10887556 | SRX7556537 | SRS5993923 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CGCACC: hair cells wt 2F7 | GSM4271736 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CGCACC: hair cells wt 2F7 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271736 | GSM4271736: CGCACC: hair cells wt 2F7; Danio rerio; RNA Seq | GSM4271736 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271736 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CGCACC_r1.fq.gz GEO_CGCACC_r2.fq.gz | fastq fastq | 59064720.0 | 894920.0 | GSM4271736 r1 | 0:16 1:50 | A:15436523;C:14686266;G:14017782;T:14906469;N:17680 | 16 | 50 | 15436523 | 14686266 | 14017782 | 14906469 | 17680 | SRX7556537 | SRS5993923 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.81502 | 0.0 | 0.16399 | 1.0 | 0.97847 | 0.41105 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56155 | 56155 | SRR10887555 | SRX7556536 | SRS5993921 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CCACCG: hair cells wt 2E12 | GSM4271735 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CCACCG: hair cells wt 2E12 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271735 | GSM4271735: CCACCG: hair cells wt 2E12; Danio rerio; RNA Seq | GSM4271735 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271735 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CCACCG_r1.fq.gz GEO_CCACCG_r2.fq.gz | fastq fastq | 28334064.0 | 429304.0 | GSM4271735 r1 | 0:16 1:50 | A:7520223;C:7025285;G:6745861;T:7033764;N:8931 | 16 | 50 | 7520223 | 7025285 | 6745861 | 7033764 | 8931 | SRX7556536 | SRS5993921 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.80711 | 0.0 | 0.10281 | 1.0 | 0.97968 | 0.36993 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56156 | 56156 | SRR10887554 | SRX7556535 | SRS5993920 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CAGCCG: hair cells wt 2E11 | GSM4271734 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CAGCCG: hair cells wt 2E11 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271734 | GSM4271734: CAGCCG: hair cells wt 2E11; Danio rerio; RNA Seq | GSM4271734 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271734 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CAGCCG_r1.fq.gz GEO_CAGCCG_r2.fq.gz | fastq fastq | 76943724.0 | 1165814.0 | GSM4271734 r1 | 0:16 1:50 | A:20252257;C:18252609;G:19289676;T:19127181;N:22001 | 16 | 50 | 20252257 | 18252609 | 19289676 | 19127181 | 22001 | SRX7556535 | SRS5993920 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.82968 | 0.0 | 0.07998 | 1.0 | 0.98098 | 0.47591 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56157 | 56157 | SRR10887553 | SRX7556534 | SRS5993919 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CACCCC: hair cells wt 2E10 | GSM4271733 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CACCCC: hair cells wt 2E10 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271733 | GSM4271733: CACCCC: hair cells wt 2E10; Danio rerio; RNA Seq | GSM4271733 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271733 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CACCCC_r1.fq.gz GEO_CACCCC_r2.fq.gz | fastq fastq | 59700300.0 | 904550.0 | GSM4271733 r1 | 0:16 1:50 | A:15645395;C:15522037;G:13562532;T:14955831;N:14505 | 16 | 50 | 15645395 | 15522037 | 13562532 | 14955831 | 14505 | SRX7556534 | SRS5993919 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.74633 | 0.0 | 0.15499 | 1.0 | 0.97084 | 0.51247 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56158 | 56158 | SRR10887552 | SRX7556533 | SRS5993924 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | AGGCCC: hair cells wt 2E9 | GSM4271732 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | AGGCCC: hair cells wt 2E9 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271732 | GSM4271732: AGGCCC: hair cells wt 2E9; Danio rerio; RNA Seq | GSM4271732 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271732 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_AGGCCC_r1.fq.gz GEO_AGGCCC_r2.fq.gz | fastq fastq | 247661106.0 | 3752441.0 | GSM4271732 r1 | 0:16 1:50 | A:60796649;C:61932057;G:69774659;T:55097229;N:60512 | 16 | 50 | 60796649 | 61932057 | 69774659 | 55097229 | 60512 | SRX7556533 | SRS5993924 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.67963 | 0.0 | 0.14932 | 1.0 | 0.9656 | 0.55686 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56159 | 56159 | SRR10887551 | SRX7556532 | SRS5993918 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | AGCCCG: hair cells wt 2E8 | GSM4271731 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | AGCCCG: hair cells wt 2E8 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271731 | GSM4271731: AGCCCG: hair cells wt 2E8; Danio rerio; RNA Seq | GSM4271731 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271731 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_AGCCCG_r1.fq.gz GEO_AGCCCG_r2.fq.gz | fastq fastq | 85194054.0 | 1290819.0 | GSM4271731 r1 | 0:16 1:50 | A:21886276;C:20333936;G:22929730;T:20024600;N:19512 | 16 | 50 | 21886276 | 20333936 | 22929730 | 20024600 | 19512 | SRX7556532 | SRS5993918 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.77493 | 0.0 | 0.12576 | 1.0 | 0.97007 | 0.54242 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56160 | 56160 | SRR10887550 | SRX7556531 | SRS5993931 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | ACGCCG: hair cells wt 2E7 | GSM4271730 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | ACGCCG: hair cells wt 2E7 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271730 | GSM4271730: ACGCCG: hair cells wt 2E7; Danio rerio; RNA Seq | GSM4271730 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271730 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_ACGCCG_r1.fq.gz GEO_ACGCCG_r2.fq.gz | fastq fastq | 16576230.0 | 251155.0 | GSM4271730 r1 | 0:16 1:50 | A:4101131;C:3992983;G:4977837;T:3500149;N:4130 | 16 | 50 | 4101131 | 3992983 | 4977837 | 3500149 | 4130 | SRX7556531 | SRS5993931 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.22521 | 0.0 | 0.11583 | 1.0 | 0.97652 | 0.49987 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56161 | 56161 | SRR10887549 | SRX7556530 | SRS5993922 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CTTCTG: hair cells wt 2D12 | GSM4271729 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CTTCTG: hair cells wt 2D12 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271729 | GSM4271729: CTTCTG: hair cells wt 2D12; Danio rerio; RNA Seq | GSM4271729 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271729 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CTTCTG_r1.fq.gz GEO_CTTCTG_r2.fq.gz | fastq fastq | 10296198.0 | 156003.0 | GSM4271729 r1 | 0:16 1:50 | A:2532051;C:2299039;G:2378957;T:3082993;N:3158 | 16 | 50 | 2532051 | 2299039 | 2378957 | 3082993 | 3158 | SRX7556530 | SRS5993922 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.8312 | 0.0 | 0.10552 | 1.0 | 0.98271 | 0.50933 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56162 | 56162 | SRR10887548 | SRX7556529 | SRS5993916 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CCGATT: hair cells wt 2D11 | GSM4271728 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CCGATT: hair cells wt 2D11 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271728 | GSM4271728: CCGATT: hair cells wt 2D11; Danio rerio; RNA Seq | GSM4271728 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271728 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CCGATT_r1.fq.gz GEO_CCGATT_r2.fq.gz | fastq fastq | 62508666.0 | 947101.0 | GSM4271728 r1 | 0:16 1:50 | A:16582399;C:13664923;G:14482786;T:17761639;N:16919 | 16 | 50 | 16582399 | 13664923 | 14482786 | 17761639 | 16919 | SRX7556529 | SRS5993916 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.88829 | 0.0 | 0.24871 | 1.0 | 0.98171 | 0.52749 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56163 | 56163 | SRR10887547 | SRX7556528 | SRS5993915 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CAGTCA: hair cells wt 2D10 | GSM4271727 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CAGTCA: hair cells wt 2D10 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271727 | GSM4271727: CAGTCA: hair cells wt 2D10; Danio rerio; RNA Seq | GSM4271727 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271727 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CAGTCA_r1.fq.gz GEO_CAGTCA_r2.fq.gz | fastq fastq | 81890886.0 | 1240771.0 | GSM4271727 r1 | 0:16 1:50 | A:22385298;C:18267104;G:18858387;T:22355623;N:24474 | 16 | 50 | 22385298 | 18267104 | 18858387 | 22355623 | 24474 | SRX7556528 | SRS5993915 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.84616 | 0.0 | 0.08088 | 1.0 | 0.98121 | 0.43702 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56164 | 56164 | SRR10887546 | SRX7556527 | SRS5993912 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | AGGGAT: hair cells wt 2D9 | GSM4271726 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | AGGGAT: hair cells wt 2D9 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271726 | GSM4271726: AGGGAT: hair cells wt 2D9; Danio rerio; RNA Seq | GSM4271726 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271726 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_AGGGAT_r1.fq.gz GEO_AGGGAT_r2.fq.gz | fastq fastq | 27941364.0 | 423354.0 | GSM4271726 r1 | 0:16 1:50 | A:7658771;C:5529411;G:7466727;T:7278034;N:8421 | 16 | 50 | 7658771 | 5529411 | 7466727 | 7278034 | 8421 | SRX7556527 | SRS5993912 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.71935 | 0.0 | 0.14115 | 1.0 | 0.98021 | 0.39706 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56165 | 56165 | SRR10887545 | SRX7556526 | SRS5993917 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TCTTTC: hair cells wt 2D8 | GSM4271725 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TCTTTC: hair cells wt 2D8 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271725 | GSM4271725: TCTTTC: hair cells wt 2D8; Danio rerio; RNA Seq | GSM4271725 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271725 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TCTTTC_r1.fq.gz GEO_TCTTTC_r2.fq.gz | fastq fastq | 39611286.0 | 600171.0 | GSM4271725 r1 | 0:16 1:50 | A:9593653;C:8891817;G:9379515;T:11735763;N:10538 | 16 | 50 | 9593653 | 8891817 | 9379515 | 11735763 | 10538 | SRX7556526 | SRS5993917 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.7029 | 0.0 | 0.09623 | 1.0 | 0.98005 | 0.5794 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56166 | 56166 | SRR10887544 | SRX7556525 | SRS5993911 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TTTGTA: hair cells wt 2D7 | GSM4271724 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TTTGTA: hair cells wt 2D7 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271724 | GSM4271724: TTTGTA: hair cells wt 2D7; Danio rerio; RNA Seq | GSM4271724 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271724 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TTTGTA_r1.fq.gz GEO_TTTGTA_r2.fq.gz | fastq fastq | 45225048.0 | 685228.0 | GSM4271724 r1 | 0:16 1:50 | A:11889541;C:8360740;G:10779684;T:14183435;N:11648 | 16 | 50 | 11889541 | 8360740 | 10779684 | 14183435 | 11648 | SRX7556525 | SRS5993911 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.81562 | 0.0 | 0.09419 | 1.0 | 0.97916 | 0.51242 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56167 | 56167 | SRR10887543 | SRX7556524 | SRS5993910 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TGTAAA: hair cells wt 2C12 | GSM4271723 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TGTAAA: hair cells wt 2C12 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271723 | GSM4271723: TGTAAA: hair cells wt 2C12; Danio rerio; RNA Seq | GSM4271723 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271723 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TGTAAA_r1.fq.gz GEO_TGTAAA_r2.fq.gz | fastq fastq | 36393456.0 | 551416.0 | GSM4271723 r1 | 0:16 1:50 | A:10494740;C:6916737;G:8340339;T:10629953;N:11687 | 16 | 50 | 10494740 | 6916737 | 8340339 | 10629953 | 11687 | SRX7556524 | SRS5993910 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.88673 | 0.0 | 0.07491 | 1.0 | 0.9867 | 0.42572 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Multi-stage | Multi-stage | Lateral Line | Sensory System | |||||||||||
| 56168 | 56168 | SRR10887542 | SRX7556523 | SRS5993909 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TGAAAT: hair cells wt 2C11 | GSM4271722 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TGAAAT: hair cells wt 2C11 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271722 | GSM4271722: TGAAAT: hair cells wt 2C11; Danio rerio; RNA Seq | GSM4271722 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271722 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TGAAAT_r1.fq.gz GEO_TGAAAT_r2.fq.gz | fastq fastq | 59922720.0 | 907920.0 | GSM4271722 r1 | 0:16 1:50 | A:17660178;C:11271616;G:13597589;T:17378574;N:14763 | 16 | 50 | 17660178 | 11271616 | 13597589 | 17378574 | 14763 | SRX7556523 | SRS5993909 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.86668 | 0.0 | 0.13202 | 1.0 | 0.98466 | 0.47258 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Multi-stage | Multi-stage | Lateral Line | Sensory System | |||||||||||
| 56169 | 56169 | SRR10887541 | SRX7556522 | SRS5993914 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TCATTA: hair cells wt 2C10 | GSM4271721 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TCATTA: hair cells wt 2C10 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271721 | GSM4271721: TCATTA: hair cells wt 2C10; Danio rerio; RNA Seq | GSM4271721 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271721 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TCATTA_r1.fq.gz GEO_TCATTA_r2.fq.gz | fastq fastq | 46021734.0 | 697299.0 | GSM4271721 r1 | 0:16 1:50 | A:12725573;C:9548168;G:10202938;T:13533019;N:12036 | 16 | 50 | 12725573 | 9548168 | 10202938 | 13533019 | 12036 | SRX7556522 | SRS5993914 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.79991 | 0.0 | 0.12416 | 1.0 | 0.98285 | 0.51119 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Multi-stage | Multi-stage | Lateral Line | Sensory System | |||||||||||
| 56170 | 56170 | SRR10887540 | SRX7556521 | SRS5993907 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TATTTG: hair cells wt 2C9 | GSM4271720 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TATTTG: hair cells wt 2C9 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271720 | GSM4271720: TATTTG: hair cells wt 2C9; Danio rerio; RNA Seq | GSM4271720 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271720 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TATTTG_r1.fq.gz GEO_TATTTG_r2.fq.gz | fastq fastq | 57077328.0 | 864808.0 | GSM4271720 r1 | 0:16 1:50 | A:15095956;C:10660095;G:12874801;T:18430756;N:15720 | 16 | 50 | 15095956 | 10660095 | 12874801 | 18430756 | 15720 | SRX7556521 | SRS5993907 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.83235 | 0.0 | 0.08647 | 1.0 | 0.98411 | 0.4321 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Multi-stage | Multi-stage | Lateral Line | Sensory System | |||||||||||
| 56171 | 56171 | SRR10887539 | SRX7556520 | SRS5993906 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TATGTT: hair cells wt 2C8 | GSM4271719 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TATGTT: hair cells wt 2C8 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271719 | GSM4271719: TATGTT: hair cells wt 2C8; Danio rerio; RNA Seq | GSM4271719 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271719 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TATGTT_r1.fq.gz GEO_TATGTT_r2.fq.gz | fastq fastq | 82334538.0 | 1247493.0 | GSM4271719 r1 | 0:16 1:50 | A:21259201;C:15330189;G:20495066;T:25226866;N:23216 | 16 | 50 | 21259201 | 15330189 | 20495066 | 25226866 | 23216 | SRX7556520 | SRS5993906 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.82387 | 0.0 | 0.08807 | 1.0 | 0.97707 | 0.53859 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Multi-stage | Multi-stage | Lateral Line | Sensory System | |||||||||||
| 56172 | 56172 | SRR10887538 | SRX7556519 | SRS5993904 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | TATATC: hair cells wt 2C7 | GSM4271718 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | TATATC: hair cells wt 2C7 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271718 | GSM4271718: TATATC: hair cells wt 2C7; Danio rerio; RNA Seq | GSM4271718 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271718 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_TATATC_r1.fq.gz GEO_TATATC_r2.fq.gz | fastq fastq | 47552802.0 | 720497.0 | GSM4271718 r1 | 0:16 1:50 | A:13161599;C:9865238;G:10361619;T:14152235;N:12111 | 16 | 50 | 13161599 | 9865238 | 10361619 | 14152235 | 12111 | SRX7556519 | SRS5993904 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.80675 | 0.0 | 0.09336 | 1.0 | 0.98466 | 0.43652 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Multi-stage | Multi-stage | Lateral Line | Sensory System | |||||||||||
| 56173 | 56173 | SRR10887537 | SRX7556518 | SRS5993903 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GTATAA: hair cells wt 2B12 | GSM4271717 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GTATAA: hair cells wt 2B12 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271717 | GSM4271717: GTATAA: hair cells wt 2B12; Danio rerio; RNA Seq | GSM4271717 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271717 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GTATAA_r1.fq.gz GEO_GTATAA_r2.fq.gz | fastq fastq | 105576240.0 | 1599640.0 | GSM4271717 r1 | 0:16 1:50 | A:30487024;C:19765998;G:24257759;T:31040963;N:24496 | 16 | 50 | 30487024 | 19765998 | 24257759 | 31040963 | 24496 | SRX7556518 | SRS5993903 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.8655 | 0.0 | 0.10874 | 1.0 | 0.97729 | 0.45045 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56174 | 56174 | SRR10887536 | SRX7556517 | SRS5993902 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GATATA: hair cells wt 2B11 | GSM4271716 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GATATA: hair cells wt 2B11 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271716 | GSM4271716: GATATA: hair cells wt 2B11; Danio rerio; RNA Seq | GSM4271716 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271716 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GATATA_r1.fq.gz GEO_GATATA_r2.fq.gz | fastq fastq | 131727882.0 | 1995877.0 | GSM4271716 r1 | 0:16 1:50 | A:39145090;C:25049441;G:28985366;T:38514286;N:33699 | 16 | 50 | 39145090 | 25049441 | 28985366 | 38514286 | 33699 | SRX7556517 | SRS5993902 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.91406 | 0.0 | 0.57766 | 1.0 | 0.98425 | 0.43543 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56175 | 56175 | SRR10887535 | SRX7556516 | SRS5993901 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GAAATT: hair cells wt 2B10 | GSM4271715 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GAAATT: hair cells wt 2B10 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271715 | GSM4271715: GAAATT: hair cells wt 2B10; Danio rerio; RNA Seq | GSM4271715 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271715 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GAAATT_r1.fq.gz GEO_GAAATT_r2.fq.gz | fastq fastq | 33507144.0 | 507684.0 | GSM4271715 r1 | 0:16 1:50 | A:9768700;C:6465594;G:7741672;T:9522644;N:8534 | 16 | 50 | 9768700 | 6465594 | 7741672 | 9522644 | 8534 | SRX7556516 | SRS5993901 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.7961 | 0.0 | 0.12613 | 1.0 | 0.98169 | 0.50881 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56176 | 56176 | SRR10887534 | SRX7556515 | SRS5993908 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CTATTA: hair cells wt 2B9 | GSM4271714 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CTATTA: hair cells wt 2B9 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271714 | GSM4271714: CTATTA: hair cells wt 2B9; Danio rerio; RNA Seq | GSM4271714 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271714 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CTATTA_r1.fq.gz GEO_CTATTA_r2.fq.gz | fastq fastq | 48644112.0 | 737032.0 | GSM4271714 r1 | 0:16 1:50 | A:13431743;C:10100159;G:10510510;T:14590743;N:10957 | 16 | 50 | 13431743 | 10100159 | 10510510 | 14590743 | 10957 | SRX7556515 | SRS5993908 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.82941 | 0.0 | 0.09209 | 1.0 | 0.98171 | 0.48275 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56177 | 56177 | SRR10887533 | SRX7556514 | SRS5993913 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CATTTA: hair cells wt 2B8 | GSM4271713 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CATTTA: hair cells wt 2B8 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271713 | GSM4271713: CATTTA: hair cells wt 2B8; Danio rerio; RNA Seq | GSM4271713 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271713 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CATTTA_r1.fq.gz GEO_CATTTA_r2.fq.gz | fastq fastq | 149976486.0 | 2272371.0 | GSM4271713 r1 | 0:16 1:50 | A:42208515;C:30318978;G:31462869;T:45953123;N:33001 | 16 | 50 | 42208515 | 30318978 | 31462869 | 45953123 | 33001 | SRX7556514 | SRS5993913 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.87297 | 0.0 | 0.07359 | 1.0 | 0.97839 | 0.41133 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56178 | 56178 | SRR10887532 | SRX7556513 | SRS5993900 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | CAATAA: hair cells wt 2B7 | GSM4271712 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | CAATAA: hair cells wt 2B7 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271712 | GSM4271712: CAATAA: hair cells wt 2B7; Danio rerio; RNA Seq | GSM4271712 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271712 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_CAATAA_r1.fq.gz GEO_CAATAA_r2.fq.gz | fastq fastq | 57412542.0 | 869887.0 | GSM4271712 r1 | 0:16 1:50 | A:17908670;C:11429509;G:11963221;T:16094209;N:16933 | 16 | 50 | 17908670 | 11429509 | 11963221 | 16094209 | 16933 | SRX7556513 | SRS5993900 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.84753 | 0.0 | 0.12124 | 1.0 | 0.98427 | 0.40643 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56179 | 56179 | SRR10887531 | SRX7556512 | SRS5993905 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | ATACTT: hair cells wt 2A12 | GSM4271711 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | ATACTT: hair cells wt 2A12 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271711 | GSM4271711: ATACTT: hair cells wt 2A12; Danio rerio; RNA Seq | GSM4271711 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271711 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_ATACTT_r1.fq.gz GEO_ATACTT_r2.fq.gz | fastq fastq | 8651148.0 | 131078.0 | GSM4271711 r1 | 0:16 1:50 | A:2330634;C:1784107;G:2159176;T:2374901;N:2330 | 16 | 50 | 2330634 | 1784107 | 2159176 | 2374901 | 2330 | SRX7556512 | SRS5993905 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.29454 | 0.0 | 0.1535 | 1.0 | 0.9865 | 0.65013 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56180 | 56180 | SRR10887530 | SRX7556511 | SRS5993898 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | ATAACA: hair cells wt 2A11 | GSM4271710 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | ATAACA: hair cells wt 2A11 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271710 | GSM4271710: ATAACA: hair cells wt 2A11; Danio rerio; RNA Seq | GSM4271710 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271710 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_ATAACA_r1.fq.gz GEO_ATAACA_r2.fq.gz | fastq fastq | 58610706.0 | 888041.0 | GSM4271710 r1 | 0:16 1:50 | A:18014874;C:11661118;G:12339527;T:16578759;N:16428 | 16 | 50 | 18014874 | 11661118 | 12339527 | 16578759 | 16428 | SRX7556511 | SRS5993898 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.81794 | 0.0 | 0.0639 | 1.0 | 0.98563 | 0.46396 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56181 | 56181 | SRR10887529 | SRX7556510 | SRS5993897 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | AGTAAT: hair cells wt 2A10 | GSM4271709 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | AGTAAT: hair cells wt 2A10 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271709 | GSM4271709: AGTAAT: hair cells wt 2A10; Danio rerio; RNA Seq | GSM4271709 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271709 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_AGTAAT_r1.fq.gz GEO_AGTAAT_r2.fq.gz | fastq fastq | 111276594.0 | 1686009.0 | GSM4271709 r1 | 0:16 1:50 | A:32926054;C:20521030;G:24191119;T:33604147;N:34244 | 16 | 50 | 32926054 | 20521030 | 24191119 | 33604147 | 34244 | SRX7556510 | SRS5993897 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.88188 | 0.0 | 0.14223 | 1.0 | 0.98005 | 0.44365 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56182 | 56182 | SRR10887528 | SRX7556509 | SRS5993896 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | ACTTTA: hair cells wt 2A9 | GSM4271708 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | ACTTTA: hair cells wt 2A9 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271708 | GSM4271708: ACTTTA: hair cells wt 2A9; Danio rerio; RNA Seq | GSM4271708 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271708 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_ACTTTA_r1.fq.gz GEO_ACTTTA_r2.fq.gz | fastq fastq | 61468308.0 | 931338.0 | GSM4271708 r1 | 0:16 1:50 | A:17145659;C:12322061;G:13013829;T:18971733;N:15026 | 16 | 50 | 17145659 | 12322061 | 13013829 | 18971733 | 15026 | SRX7556509 | SRS5993896 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.79407 | 0.0 | 0.09895 | 1.0 | 0.98313 | 0.41971 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56183 | 56183 | SRR10887527 | SRX7556508 | SRS5993894 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | ACATAA: hair cells wt 2A8 | GSM4271707 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | ACATAA: hair cells wt 2A8 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271707 | GSM4271707: ACATAA: hair cells wt 2A8; Danio rerio; RNA Seq | GSM4271707 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271707 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_ACATAA_r1.fq.gz GEO_ACATAA_r2.fq.gz | fastq fastq | 158605656.0 | 2403116.0 | GSM4271707 r1 | 0:16 1:50 | A:49247323;C:32258174;G:34033114;T:43023807;N:43238 | 16 | 50 | 49247323 | 32258174 | 34033114 | 43023807 | 43238 | SRX7556508 | SRS5993894 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.81999 | 0.0 | 0.11125 | 1.0 | 0.97904 | 0.47654 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56184 | 56184 | SRR10887526 | SRX7556507 | SRS5993899 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | AATTGA: hair cells wt 2A7 | GSM4271706 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | AATTGA: hair cells wt 2A7 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271706 | GSM4271706: AATTGA: hair cells wt 2A7; Danio rerio; RNA Seq | GSM4271706 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271706 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_AATTGA_r1.fq.gz GEO_AATTGA_r2.fq.gz | fastq fastq | 51021498.0 | 773053.0 | GSM4271706 r1 | 0:16 1:50 | A:14658299;C:10020932;G:12806777;T:13520360;N:15130 | 16 | 50 | 14658299 | 10020932 | 12806777 | 13520360 | 15130 | SRX7556507 | SRS5993899 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.5837 | 0.0 | 0.13118 | 1.0 | 0.98324 | 0.53616 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System | |||||||||||
| 56185 | 56185 | SRR10887525 | SRX7556506 | SRS5993892 | SRP241937 | PRJNA601204 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE143663 | Transcriptome Analysis | This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae. | pubmed:32109392 | GGGCTC: hair cells Emx2 mutant 4H5 | GSM4271705 | source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] Emx2 mutant|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GGGCTC: hair cells Emx2 mutant 4H5 | Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table | zebrafish neuromast hair cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP] Emx2 mutant|tissue:zebrafish neuromast hair cells|developmental day:6 dpf | GSM4271705 | GSM4271705: GGGCTC: hair cells Emx2 mutant 4H5; Danio rerio; RNA Seq | GSM4271705 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 | GEO Accession:GSM4271705 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP241937 | GEO_GGGCTC_r1.fq.gz GEO_GGGCTC_r2.fq.gz | fastq fastq | 14613588.0 | 221418.0 | GSM4271705 r1 | 0:16 1:50 | A:3780247;C:3111579;G:3578982;T:4138632;N:4148 | 16 | 50 | 3780247 | 3111579 | 3578982 | 4138632 | 4148 | SRX7556506 | SRS5993892 | SRA1026350 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.0 | 0.79993 | 0.0 | 0.32776 | 1.0 | 0.98088 | 0.70912 | 16 | 50 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2020-01-14 | Larval | Larval | Lateral Line | Sensory System |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;