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236 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" and tissue_curation = "Embryo Imprecise"

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devstage_curation 7

experiment.library_strategy 3

devstage_curation_coarse 3

experiment.library_selection 2

tissue_curation_coarse 1

tissue_curation 1

  • Embryo Imprecise · 236 ✖

technology 1

  • 10x · 236 ✖

experiment.platform 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 236 ✖

experiment.library_layout 1

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
30012 30012 SRR28164886 SRX23795142 SRS20618185 SRP485064 PRJNA1067370 zebrafish embryo for scRNA seq and bulk RNA seq PRJNA1067370 Other Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.     10x Genomics multiplexing CMO scRNA seq wild type and hamp / 36 hpf CMO Zebrafish embryo scRNA seq wild type and hamp / 36 hpf CMO   strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf CMO|dev stage:36 hpf CMO|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:WT/hamp knockdown|sample type:whole organism|BioSampleModel:Model organism or animal                 scRNA seq wild type and hamp / 36 hpf CMO C 3 C 3 10x Genomics multiplexing CMO     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     36h_Multiplexing_Capture_S1_L001_R2_001.fastq.gz 36h_Multiplexing_Capture_S1_L001_R1_001.fastq.gz fastq fastq 42856660500.0 142855535.0 36h Multiplexing Capture S1 L001 R1 001.fastq.gz 0:150 1:150 A:8992350191;C:10354632010;G:13923089582;T:9585439035;N:1149682 150 150     8992350191 10354632010 13923089582 9585439035 1149682 SRX23795142 SRS20618185 SRA1813495 Shanghai Ocean University|College of Fisheries and Life Shanghai Ocean University 2 0.0 0.0 0.0 0.0 1.0 1.0     150 150 T T mates < 9% mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2024-02-29 Pharyngula Embryo Embryo Imprecise All anatomical structures
30013 30013 SRR28164887 SRX23795141 SRS20618186 SRP485064 PRJNA1067370 zebrafish embryo for scRNA seq and bulk RNA seq PRJNA1067370 Other Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.     10x Genomics multiplexing CMO scRNA seq wild type and hamp / 24 hpf CMO Zebrafish embryo scRNA seq wild type and hamp / 24 hpf CMO   strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:24 hpf CMO|dev stage:24 hpf CMO|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:WT/hamp knockdown|sample type:whole organism|BioSampleModel:Model organism or animal                 scRNA seq wild type and hamp / 24 hpf CMO C 2 C 2 10x Genomics multiplexing CMO     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     24h_Multiplexing_Capture_S1_L001_R2_001.fastq.gz 24h_Multiplexing_Capture_S1_L001_R1_001.fastq.gz fastq fastq 45212181900.0 150707273.0 24h Multiplexing Capture S1 L001 R1 001.fastq.gz 0:150 1:150 A:9741878752;C:11183590476;G:14447932886;T:9837582173;N:1197613 150 150     9741878752 11183590476 14447932886 9837582173 1197613 SRX23795141 SRS20618186 SRA1813495 Shanghai Ocean University|College of Fisheries and Life Shanghai Ocean University 2 0.0 0.0 0.0 0.0 1.0 1.0     150 150 T T mates < 9% mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2024-02-29 Pharyngula Embryo Embryo Imprecise All anatomical structures
30014 30014 SRR28164888 SRX23795140 SRS20618184 SRP485064 PRJNA1067370 zebrafish embryo for scRNA seq and bulk RNA seq PRJNA1067370 Other Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.     10x Genomics multiplexing CMO scRNA seq wild type and hamp / 12 hpf CMO Zebrafish embryo scRNA seq wild type and hamp / 12 hpf CMO   strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:12 hpf CMO|dev stage:12 hpf CMO|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:WT/hamp knockdown|sample type:whole organism|BioSampleModel:Model organism or animal                 scRNA seq wild type and hamp / 12 hpf CMO C 1 C 1 10x Genomics multiplexing CMO     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     12h_Multiplexing_Capture_S1_L001_R2_001.fastq.gz 12h_Multiplexing_Capture_S1_L001_R1_001.fastq.gz fastq fastq 23801259900.0 79337533.0 12h Multiplexing Capture S1 L001 R1 001.fastq.gz 0:150 1:150 A:5110000752;C:5818733743;G:7758205963;T:5113684708;N:634734 150 150     5110000752 5818733743 7758205963 5113684708 634734 SRX23795140 SRS20618184 SRA1813495 Shanghai Ocean University|College of Fisheries and Life Shanghai Ocean University 2 0.0 0.0 0.0 0.0 1.0 1.0     150 150 T T mates < 9% mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2024-02-29 Segmentation Embryo Embryo Imprecise All anatomical structures
30015 30015 SRR28164889 SRX23795139 SRS20618183 SRP485064 PRJNA1067370 zebrafish embryo for scRNA seq and bulk RNA seq PRJNA1067370 Other Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.     10x Genomics multiplexing GEX scRNA seq wild type and hamp / 36 hpf GEX Zebrafish embryo scRNA seq wild type and hamp / 36 hpf GEX   strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf GEX|dev stage:36 hpf GEX|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:WT/hamp knockdown|sample type:whole organism|BioSampleModel:Model organism or animal                 scRNA seq wild type and hamp / 36 hpf GEX G 3 G 3 10x Genomics multiplexing GEX     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     36h_Gene_Expression_S1_L001_R2_001.fastq.gz 36h_Gene_Expression_S1_L001_R1_001.fastq.gz fastq fastq 140285088600.0 467616962.0 36h Gene Expression S1 L001 R1 001.fastq.gz 0:150 1:150 A:41651884464;C:24916307056;G:25991077208;T:47722140024;N:3679848 150 150     41651884464 24916307056 25991077208 47722140024 3679848 SRX23795139 SRS20618183 SRA1813495 Shanghai Ocean University|College of Fisheries and Life Shanghai Ocean University 2 0.00148 0.91873 0.0 0.15509 0.99985 0.78086 0.57142 0.52919 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2024-02-29 Pharyngula Embryo Embryo Imprecise All anatomical structures
30016 30016 SRR28164890 SRX23795138 SRS20618182 SRP485064 PRJNA1067370 zebrafish embryo for scRNA seq and bulk RNA seq PRJNA1067370 Other Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.     10x Genomics multiplexing GEX scRNA seq wild type and hamp / 24 hpf GEX Zebrafish embryo scRNA seq wild type and hamp / 24 hpf GEX   strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:24 hpf GEX|dev stage:24 hpf GEX|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:WT/hamp knockdown|sample type:whole organism|BioSampleModel:Model organism or animal                 scRNA seq wild type and hamp / 24 hpf GEX G 2 G 2 10x Genomics multiplexing GEX     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     24h_Gene_Expression_S1_L001_R1_001.fastq.gz 24h_Gene_Expression_S1_L001_R2_001.fastq.gz fastq fastq 147407645100.0 491358817.0 24h Gene Expression S1 L001 R1 001.fastq.gz 0:150 1:150 A:43802123106;C:26617386219;G:27720887375;T:49263400239;N:3848161 150 150     43802123106 26617386219 27720887375 49263400239 3848161 SRX23795138 SRS20618182 SRA1813495 Shanghai Ocean University|College of Fisheries and Life Shanghai Ocean University 2 0.00129 0.92038 0.00042 0.15021 0.99993 0.77581 0.33333 0.51584 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2024-02-29 Pharyngula Embryo Embryo Imprecise All anatomical structures
30017 30017 SRR28164891 SRX23795137 SRS20618181 SRP485064 PRJNA1067370 zebrafish embryo for scRNA seq and bulk RNA seq PRJNA1067370 Other Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.     10x Genomics multiplexing GEX scRNA seq wild type and hamp / 12 hpf GEX Zebrafish embryo scRNA seq wild type and hamp / 12 hpf GEX   strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:12 hpf GEX|dev stage:12 hpf GEX|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:WT/hamp knockdown|sample type:whole organism|BioSampleModel:Model organism or animal                 scRNA seq wild type and hamp / 12 hpf GEX G 1 G 1 10x Genomics multiplexing GEX     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     12h_Gene_Expression_S1_L001_R2_001.fastq.gz 12h_Gene_Expression_S1_L001_R1_001.fastq.gz fastq fastq 204426398700.0 681421329.0 12h Gene Expression S1 L001 R1 001.fastq.gz 0:150 1:150 A:61302872939;C:35072603645;G:37153666376;T:70891933893;N:5321847 150 150     61302872939 35072603645 37153666376 70891933893 5321847 SRX23795137 SRS20618181 SRA1813495 Shanghai Ocean University|College of Fisheries and Life Shanghai Ocean University 2 0.00085 0.9058 0.0 0.12081 0.99991 0.80231 0.5 0.52456 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2024-02-29 Segmentation Embryo Embryo Imprecise All anatomical structures
32783 32783 SRR29438460 SRX24951082 SRS21654793 SRP514388 PRJNA1124950 Deciphering the Toxic Effects of Polystyrene Nanoparticle on Erythropoiesis at Single Cell Resolution GSE270075 Transcriptome Analysis The toxic effects of polystyrene nanoparticles on aquatic ecosystems have been predominantly studied with a focus on oxidative stress and inflammatory responses. However this study comprehensively examined the effects of polystyrene nanoparticles on the development of zebrafish embryos using single cell RNA sequencing analysis explicitly investigating their effects on erythropoiesis. In vivo experiments were conducted using zebrafish embryos to validate the single cell RNA sequencing analysis. Exposure to polystyrene nanoparticles resulted in a decrease in the proportion of mature erythrocytes due to an increase in immature erythrocytes during the erythrocyte differentiation process. Additionally heme synthesis was impaired leading to a decrease in the proportion of erythrocytes. These findings indicated the toxic effects of polystyrene nanoparticles on hematopoiesis. Overall design: 120 hpf zebrafish embryos were pooled as a control groupwild type and 20 nm polystyrene nanoparticles PS20nm exposed group for single cell RNA sequencing.   pubmed:39846194   Zebra PS GSM8334032   source name:embryos|tissue:embryos|Stage:120 hpf|treatment:PS20nm exposure|geo loc name:missing|collection date:missing Zebra PS First the quality and basic statistics of raw sequencing data were checked through FastQC. post the quality control process sequencing data were processed through a Cell Ranger v6.0.0 10X Genomics count pipeline using zebrafish genome GRCz11. The zebrafish genome and transcriptome information were downloaded from the Ensembl FTP server release 104 and the index was constructed by processing with the Cell Ranger mkref pipeline. The cellranger count pipeline produces gene expression matrices containing the unique molecular identifier UMI counts per gene per barcode. Also clusters with expression profiles and information on differential gene expression were generated from the pipeline. Downstream analysis was performed using Seurat version 4.3.0 in R version 4.2.2 to process data produced through 10x genomics. Assembly: GRCz11 Supplementary files format and content: Three types of processed data files are provided: barcode.tsv features.tsv matrix.mtx embryos   The samples were carefully resuspended in a cold calcium and magnesium free solution containing 0.04% BSA/PBS. Cell counting was performed using the LUNA FX7™ Automated Fluorescence Cell Counter Logos Biosystems with acridine orange AO and propidium iodide PI staining Logos Biosystems catalog number F23001. Following this the cells were processed using the Dead Cells Removal Kit Miltenyi Biotech catalog number 130 090 101 and MS columns Miltenyi Biotech catalog number 130 042 201 in accordance with the manufacturer’s guidelines. Following the guidelines of the 10x Chromium Single Cell 5’ v2 protocol 10x Genomics document number CG000331 Single Cell RNA seq libraries were generated using the 10x Chromium Controller and the Next Gem Single Cell 5’ Reagent v2 kits 10x Genomics PN 1000244. In brief the cell suspension aiming for a recovery of 10 000 cells was combined with the reverse transcription master mix and loaded along with Single Cell 5′ Gel Beads and Partitioning Oil into a Single Cell K Chip 10x Genomics PN 1000286 to create single cell Gel Bead in emulsion GEM droplets. Within these GEMs RNA transcripts from single cells were uniquely barcoded and reverse transcribed. post the GEM RT reaction where barcoded full length cDNA was synthesized from mRNA the barcoded cDNA molecules were enriched with PCR. For the preparation of the 5’ Gene Expression Library the amplified cDNA underwent a series of steps including enzymatic fragmentation end repair A tailing adapter ligation and index PCR.   tissue:embryos|Stage:120 hpf|treatment:PS20nm exposure GSM8334032 GSM8334032: Zebra PS; Danio rerio; RNA Seq GSM8334032 r1 GSM8334032 1 The samples were carefully resuspended in a cold calcium and magnesium free solution containing 0.04% BSA/PBS. Cell counting was performed using the LUNA FX7™ Automated Fluorescence Cell Counter Logos Biosystems with acridine orange AO and propidium iodide PI staining Logos Biosystems catalog number F23001. Following this the cells were processed using the Dead Cells Removal Kit Miltenyi Biotech catalog number 130 090 101 and MS columns Miltenyi Biotech catalog number 130 042 201 in accordance with the manufacturer's guidelines. Following the guidelines of the 10x Chromium Single Cell five prime v2 protocol 10x Genomics document number CG000331 Single Cell RNA seq libraries were generated using the 10x Chromium Controller and the Next Gem Single Cell five prime Reagent v2 kits 10x Genomics PN 1000244. In brief the cell suspension aiming for a recovery of 10 000 cells was combined with the reverse transcription master mix and loaded along with Single Cell 5′ Gel Beads and Partitioning Oil into a Single Cell K Chip 10x Genomics PN 1000286 to create single cell Gel Bead in emulsion GEM droplets. Within these GEMs RNA transcripts from single cells were uniquely barcoded and reverse transcribed. post the GEM RT reaction where barcoded full length cDNA was synthesized from mRNA the barcoded cDNA molecules were enriched with PCR. For the preparation of the five prime Gene Expression Library the amplified cDNA underwent a series of steps including enzymatic fragmentation end repair A tailing adapter ligation and index PCR.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP514388     Zebra_PS_S1_L003_R2_001.fastq.gz Zebra_PS_S1_L003_R1_001.fastq.gz fastq fastq 46515993156.0 400999941.0 GSM8334032 r1 0:26 1:90 A:10540890310;C:12256097063;G:11432529211;T:12270960287;N:15516285 26 90     10540890310 12256097063 11432529211 12270960287 15516285 SRX24951082 SRS21654793 SRA1904713 Pusan National University Pusan National University 2 0.07013 0.96133 0.0269 0.15067 0.98135 0.78849 0.31441 0.54509 26 90 T B sc-like readlen illumina hiseq_era 5prime cdna_unspecified unknown sc single_cell_droplet 10x   South Korea 2024-06-17 Larval Larval Embryo Imprecise All anatomical structures
32784 32784 SRR29438461 SRX24951081 SRS21654792 SRP514388 PRJNA1124950 Deciphering the Toxic Effects of Polystyrene Nanoparticle on Erythropoiesis at Single Cell Resolution GSE270075 Transcriptome Analysis The toxic effects of polystyrene nanoparticles on aquatic ecosystems have been predominantly studied with a focus on oxidative stress and inflammatory responses. However this study comprehensively examined the effects of polystyrene nanoparticles on the development of zebrafish embryos using single cell RNA sequencing analysis explicitly investigating their effects on erythropoiesis. In vivo experiments were conducted using zebrafish embryos to validate the single cell RNA sequencing analysis. Exposure to polystyrene nanoparticles resulted in a decrease in the proportion of mature erythrocytes due to an increase in immature erythrocytes during the erythrocyte differentiation process. Additionally heme synthesis was impaired leading to a decrease in the proportion of erythrocytes. These findings indicated the toxic effects of polystyrene nanoparticles on hematopoiesis. Overall design: 120 hpf zebrafish embryos were pooled as a control groupwild type and 20 nm polystyrene nanoparticles PS20nm exposed group for single cell RNA sequencing.   pubmed:39846194   Zebra Control GSM8334031   source name:embryos|tissue:embryos|Stage:120 hpf|treatment:Wild type|geo loc name:missing|collection date:missing Zebra Control First the quality and basic statistics of raw sequencing data were checked through FastQC. post the quality control process sequencing data were processed through a Cell Ranger v6.0.0 10X Genomics count pipeline using zebrafish genome GRCz11. The zebrafish genome and transcriptome information were downloaded from the Ensembl FTP server release 104 and the index was constructed by processing with the Cell Ranger mkref pipeline. The cellranger count pipeline produces gene expression matrices containing the unique molecular identifier UMI counts per gene per barcode. Also clusters with expression profiles and information on differential gene expression were generated from the pipeline. Downstream analysis was performed using Seurat version 4.3.0 in R version 4.2.2 to process data produced through 10x genomics. Assembly: GRCz11 Supplementary files format and content: Three types of processed data files are provided: barcode.tsv features.tsv matrix.mtx embryos   The samples were carefully resuspended in a cold calcium and magnesium free solution containing 0.04% BSA/PBS. Cell counting was performed using the LUNA FX7™ Automated Fluorescence Cell Counter Logos Biosystems with acridine orange AO and propidium iodide PI staining Logos Biosystems catalog number F23001. Following this the cells were processed using the Dead Cells Removal Kit Miltenyi Biotech catalog number 130 090 101 and MS columns Miltenyi Biotech catalog number 130 042 201 in accordance with the manufacturer’s guidelines. Following the guidelines of the 10x Chromium Single Cell 5’ v2 protocol 10x Genomics document number CG000331 Single Cell RNA seq libraries were generated using the 10x Chromium Controller and the Next Gem Single Cell 5’ Reagent v2 kits 10x Genomics PN 1000244. In brief the cell suspension aiming for a recovery of 10 000 cells was combined with the reverse transcription master mix and loaded along with Single Cell 5′ Gel Beads and Partitioning Oil into a Single Cell K Chip 10x Genomics PN 1000286 to create single cell Gel Bead in emulsion GEM droplets. Within these GEMs RNA transcripts from single cells were uniquely barcoded and reverse transcribed. post the GEM RT reaction where barcoded full length cDNA was synthesized from mRNA the barcoded cDNA molecules were enriched with PCR. For the preparation of the 5’ Gene Expression Library the amplified cDNA underwent a series of steps including enzymatic fragmentation end repair A tailing adapter ligation and index PCR.   tissue:embryos|Stage:120 hpf|treatment:Wild type GSM8334031 GSM8334031: Zebra Control; Danio rerio; RNA Seq GSM8334031 r1 GSM8334031 1 The samples were carefully resuspended in a cold calcium and magnesium free solution containing 0.04% BSA/PBS. Cell counting was performed using the LUNA FX7™ Automated Fluorescence Cell Counter Logos Biosystems with acridine orange AO and propidium iodide PI staining Logos Biosystems catalog number F23001. Following this the cells were processed using the Dead Cells Removal Kit Miltenyi Biotech catalog number 130 090 101 and MS columns Miltenyi Biotech catalog number 130 042 201 in accordance with the manufacturer's guidelines. Following the guidelines of the 10x Chromium Single Cell five prime v2 protocol 10x Genomics document number CG000331 Single Cell RNA seq libraries were generated using the 10x Chromium Controller and the Next Gem Single Cell five prime Reagent v2 kits 10x Genomics PN 1000244. In brief the cell suspension aiming for a recovery of 10 000 cells was combined with the reverse transcription master mix and loaded along with Single Cell 5′ Gel Beads and Partitioning Oil into a Single Cell K Chip 10x Genomics PN 1000286 to create single cell Gel Bead in emulsion GEM droplets. Within these GEMs RNA transcripts from single cells were uniquely barcoded and reverse transcribed. post the GEM RT reaction where barcoded full length cDNA was synthesized from mRNA the barcoded cDNA molecules were enriched with PCR. For the preparation of the five prime Gene Expression Library the amplified cDNA underwent a series of steps including enzymatic fragmentation end repair A tailing adapter ligation and index PCR.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP514388     Zebra_Control_S1_L002_R1_001.fastq.gz Zebra_Control_S1_L002_R2_001.fastq.gz fastq fastq 44451768632.0 383204902.0 GSM8334031 r1 0:26 1:90 A:10119968829;C:11732695259;G:10981098564;T:11603155786;N:14850194 26 90     10119968829 11732695259 10981098564 11603155786 14850194 SRX24951081 SRS21654792 SRA1904713 Pusan National University Pusan National University 2 0.07283 0.96543 0.02838 0.15165 0.98052 0.78464 0.32149 0.56384 26 90 T B sc-like readlen illumina hiseq_era 5prime cdna_unspecified unknown sc single_cell_droplet 10x   South Korea 2024-06-17 Larval Larval Embryo Imprecise All anatomical structures
48048 48048 SRR6956074 SRX3899097 SRS3136394 SRP137889 PRJNA449093 10x analysis of wild type TLAB and MZoep zebrafish embryos at 6 somite stage GSE112824 Transcriptome Analysis Wild type and MZoep zebrafish embryos were mechanically dissociated and profiled using 10x Genomics pipeline. Overall design: 10x scRNA seq was performed on visually staged mechanically dissociated embryos. Samples were combined and sequenced in one batch. parent bioproject:PRJNA417291 pubmed:29700225   MZoep zebrafish embryo 6 somite GSM3084403   tissue:Maternal Zygotic oep tz57 Mutant Embryo|genotype/variation:MZoep mutant|developmental stage:6 somite|hpf MZoep zebrafish embryo 6 somite Data was processed using Cell Ranger 2.0.2 following the pipeline posted on 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. Command "cellranger mkfastq" was called to generate demultiplexed FASTQ files from the Illumina BCL output files. Command "cellranger count" was used to align the reads to generate the bam files provided as raw data. Single cell gene barcode counts were calculated by "cellranger count" and were filtered to eliminate non cellular barcodes filtered gene barcode counts are provided as processed data. Genome build: dr82 Supplementary files format and content: Compressed folder containing filtered gene barcode matrices in Market Exchange Format MEX as outputted by "cellranger count". Maternal Zygotic oep tz57 Mutant Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated and lysed in droplets using the 10X Chromium controller. Libraries were prepared using the 10X Chromium Single Cell three prime Reagent Kit. Libraries for the two genotypes were prepared separately to incorporate different read indices. Libraries were pooled together and sequenced in one batch. Wild type Tupful longfin / AB or MZoep tz57 fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. genotype/variation:MZoep mutant|developmental stage:6 somite|hpf GSM3084403 GSM3084403: MZoep zebrafish embryo 6 somite; Danio rerio; RNA Seq GSM3084403   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated and lysed in droplets using the 10X Chromium controller. Libraries were prepared using the 10X Chromium Single Cell three prime Reagent Kit. Libraries for the two genotypes were prepared separately to incorporate different read indices. Libraries were pooled together and sequenced in one batch. GEO Accession:GSM3084403 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP137889   dangling references:treat as unmapped 10xMZoep6S_possorted_genome_bam.bam 10X Genomics bam file 6798121188.0 117208986.0 GSM3084403 r1 0:58 A:1967536512;C:1404909465;G:1675749247;T:1735311022;N:14614942 58       1967536512 1404909465 1675749247 1735311022 14614942 SRX3899097 SRS3136394 SRA683448 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.9431   0.07175   0.84439   0.49587   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2018-04-06 Segmentation Embryo Embryo Imprecise All anatomical structures
48049 48049 SRR6956073 SRX3899096 SRS3136393 SRP137889 PRJNA449093 10x analysis of wild type TLAB and MZoep zebrafish embryos at 6 somite stage GSE112824 Transcriptome Analysis Wild type and MZoep zebrafish embryos were mechanically dissociated and profiled using 10x Genomics pipeline. Overall design: 10x scRNA seq was performed on visually staged mechanically dissociated embryos. Samples were combined and sequenced in one batch. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo 6 somite GSM3084402   tissue:Wild type TLAB Embryo|genotype/variation:wild type TLAB|developmental stage:6 somite|hpf WT zebrafish embryo 6 somite Data was processed using Cell Ranger 2.0.2 following the pipeline posted on 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. Command "cellranger mkfastq" was called to generate demultiplexed FASTQ files from the Illumina BCL output files. Command "cellranger count" was used to align the reads to generate the bam files provided as raw data. Single cell gene barcode counts were calculated by "cellranger count" and were filtered to eliminate non cellular barcodes filtered gene barcode counts are provided as processed data. Genome build: dr82 Supplementary files format and content: Compressed folder containing filtered gene barcode matrices in Market Exchange Format MEX as outputted by "cellranger count". Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated and lysed in droplets using the 10X Chromium controller. Libraries were prepared using the 10X Chromium Single Cell three prime Reagent Kit. Libraries for the two genotypes were prepared separately to incorporate different read indices. Libraries were pooled together and sequenced in one batch. Wild type Tupful longfin / AB or MZoep tz57 fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. genotype/variation:wild type TLAB|developmental stage:6 somite|hpf GSM3084402 GSM3084402: WT zebrafish embryo 6 somite; Danio rerio; RNA Seq GSM3084402   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated and lysed in droplets using the 10X Chromium controller. Libraries were prepared using the 10X Chromium Single Cell three prime Reagent Kit. Libraries for the two genotypes were prepared separately to incorporate different read indices. Libraries were pooled together and sequenced in one batch. GEO Accession:GSM3084402 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP137889   dangling references:treat as unmapped 10xWT6S_possorted_genome_bam.bam 10X Genomics bam file 9353929816.0 161274652.0 GSM3084402 r1 0:58 A:2687281275;C:1909606804;G:2337322093;T:2396497626;N:23222018 58       2687281275 1909606804 2337322093 2396497626 23222018 SRX3899096 SRS3136393 SRA683448 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.94618   0.07281   0.8435   0.501   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2018-04-06 Segmentation Embryo Embryo Imprecise All anatomical structures
49405 49405 SRR7904989 SRX4741349 SRS3822681 SRP162658 PRJNA493234 Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x] GSE120503 Other To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics. parent bioproject:PRJNA493631 pubmed:31042481;pubmed:33785593   52 hpf CHT cells GSM3402061   tissue:zebrafish embryos|region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf 52 hpf CHT cells UMI tools was used to analysis our single cell data. Firstly in “whitelist” step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts zebrafish embryos   The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture’s introduction.   region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf GSM3402061 GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq GSM3402061   1 The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture's introduction. GEO Accession:GSM3402061 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP162658     171353A_zebrafish_HSC_mixture-1_S9_L001_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-1_S9_L001_R2_001.fastq.gz fastq fastq 20612658541.0 68497783.0 GSM3402061 r1 0:150.50 1:150.43 A:5839137036;C:3293726779;G:3429783599;T:8049467865;N:543262 150 150     5839137036 3293726779 3429783599 8049467865 543262 SRX4741349 SRS3822681 SRA784241 GEO Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB) 2 0.04293 0.91361 0.0057 0.0679 0.97494 0.8187 0.48327 0.49296 150 151 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2018-09-26 Hatching Embryo Embryo Imprecise All anatomical structures
49406 49406 SRR7904990 SRX4741349 SRS3822681 SRP162658 PRJNA493234 Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x] GSE120503 Other To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics. parent bioproject:PRJNA493631 pubmed:31042481;pubmed:33785593   52 hpf CHT cells GSM3402061   tissue:zebrafish embryos|region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf 52 hpf CHT cells UMI tools was used to analysis our single cell data. Firstly in “whitelist” step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts zebrafish embryos   The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture’s introduction.   region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf GSM3402061 GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq GSM3402061   1 The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture's introduction. GEO Accession:GSM3402061 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP162658     171353A_zebrafish_HSC_mixture-1_S9_L002_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-1_S9_L002_R2_001.fastq.gz fastq fastq 20253907193.0 67305836.0 GSM3402061 r2 0:150.50 1:150.43 A:5762133423;C:3217021369;G:3378178325;T:7895841084;N:732992 150 150     5762133423 3217021369 3378178325 7895841084 732992 SRX4741349 SRS3822681 SRA784241 GEO Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB) 2 0.04531 0.91352 0.006 0.06682 0.97486 0.81889 0.47811 0.50237 151 150 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2018-09-26 Hatching Embryo Embryo Imprecise All anatomical structures
49407 49407 SRR7904991 SRX4741349 SRS3822681 SRP162658 PRJNA493234 Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x] GSE120503 Other To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics. parent bioproject:PRJNA493631 pubmed:31042481;pubmed:33785593   52 hpf CHT cells GSM3402061   tissue:zebrafish embryos|region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf 52 hpf CHT cells UMI tools was used to analysis our single cell data. Firstly in “whitelist” step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts zebrafish embryos   The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture’s introduction.   region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf GSM3402061 GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq GSM3402061   1 The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture's introduction. GEO Accession:GSM3402061 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP162658     171353A_zebrafish_HSC_mixture-2_S10_L001_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-2_S10_L001_R2_001.fastq.gz fastq fastq 27785082649.0 92332127.0 GSM3402061 r3 0:150.50 1:150.43 A:7841096067;C:4446010985;G:4651723884;T:10845511192;N:740521 150 150     7841096067 4446010985 4651723884 10845511192 740521 SRX4741349 SRS3822681 SRA784241 GEO Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB) 2 0.04331 0.91411 0.00615 0.06569 0.97445 0.81811 0.49279 0.49519 151 151 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2018-09-26 Hatching Embryo Embryo Imprecise All anatomical structures
49408 49408 SRR7904992 SRX4741349 SRS3822681 SRP162658 PRJNA493234 Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x] GSE120503 Other To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics. parent bioproject:PRJNA493631 pubmed:31042481;pubmed:33785593   52 hpf CHT cells GSM3402061   tissue:zebrafish embryos|region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf 52 hpf CHT cells UMI tools was used to analysis our single cell data. Firstly in “whitelist” step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts zebrafish embryos   The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture’s introduction.   region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf GSM3402061 GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq GSM3402061   1 The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture's introduction. GEO Accession:GSM3402061 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP162658     171353A_zebrafish_HSC_mixture-2_S10_L002_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-2_S10_L002_R2_001.fastq.gz fastq fastq 27318509546.0 90782131.0 GSM3402061 r4 0:150.50 1:150.43 A:7740943497;C:4344963417;G:4586054221;T:10645559884;N:988527 150 150     7740943497 4344963417 4586054221 10645559884 988527 SRX4741349 SRS3822681 SRA784241 GEO Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB) 2 0.04427 0.91382 0.0067 0.06513 0.97591 0.82108 0.48265 0.49507 151 151 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2018-09-26 Hatching Embryo Embryo Imprecise All anatomical structures
49409 49409 SRR7904993 SRX4741349 SRS3822681 SRP162658 PRJNA493234 Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x] GSE120503 Other To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics. parent bioproject:PRJNA493631 pubmed:31042481;pubmed:33785593   52 hpf CHT cells GSM3402061   tissue:zebrafish embryos|region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf 52 hpf CHT cells UMI tools was used to analysis our single cell data. Firstly in “whitelist” step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts zebrafish embryos   The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture’s introduction.   region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf GSM3402061 GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq GSM3402061   1 The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture's introduction. GEO Accession:GSM3402061 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP162658     171353A_zebrafish_HSC_mixture-3_S11_L001_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-3_S11_L001_R2_001.fastq.gz fastq fastq 31234027865.0 103793392.0 GSM3402061 r5 0:150.50 1:150.42 A:8823333085;C:5009305885;G:5218885705;T:12181644470;N:858720 150 150     8823333085 5009305885 5218885705 12181644470 858720 SRX4741349 SRS3822681 SRA784241 GEO Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB) 2 0.04428 0.91401 0.00582 0.06526 0.97386 0.81929 0.48301 0.48484 151 150 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2018-09-26 Hatching Embryo Embryo Imprecise All anatomical structures
49410 49410 SRR7904994 SRX4741349 SRS3822681 SRP162658 PRJNA493234 Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x] GSE120503 Other To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics. parent bioproject:PRJNA493631 pubmed:31042481;pubmed:33785593   52 hpf CHT cells GSM3402061   tissue:zebrafish embryos|region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf 52 hpf CHT cells UMI tools was used to analysis our single cell data. Firstly in “whitelist” step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts zebrafish embryos   The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture’s introduction.   region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf GSM3402061 GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq GSM3402061   1 The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture's introduction. GEO Accession:GSM3402061 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP162658     171353A_zebrafish_HSC_mixture-3_S11_L002_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-3_S11_L002_R2_001.fastq.gz fastq fastq 30613372965.0 101731210.0 GSM3402061 r6 0:150.50 1:150.43 A:8682212918;C:4881597987;G:5129046172;T:11919400304;N:1115584 150 150     8682212918 4881597987 5129046172 11919400304 1115584 SRX4741349 SRS3822681 SRA784241 GEO Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB) 2 0.04794 0.9141 0.0063 0.06497 0.97341 0.81964 0.49569 0.48688 150 149 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2018-09-26 Hatching Embryo Embryo Imprecise All anatomical structures
49411 49411 SRR7904995 SRX4741349 SRS3822681 SRP162658 PRJNA493234 Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x] GSE120503 Other To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics. parent bioproject:PRJNA493631 pubmed:31042481;pubmed:33785593   52 hpf CHT cells GSM3402061   tissue:zebrafish embryos|region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf 52 hpf CHT cells UMI tools was used to analysis our single cell data. Firstly in “whitelist” step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts zebrafish embryos   The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture’s introduction.   region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf GSM3402061 GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq GSM3402061   1 The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture's introduction. GEO Accession:GSM3402061 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP162658     171353A_zebrafish_HSC_mixture-4_S12_L001_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-4_S12_L001_R2_001.fastq.gz fastq fastq 23492564280.0 78066400.0 GSM3402061 r7 0:150.50 1:150.43 A:6598565482;C:3770698909;G:3958112639;T:9164535441;N:651809 150 150     6598565482 3770698909 3958112639 9164535441 651809 SRX4741349 SRS3822681 SRA784241 GEO Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB) 2 0.04344 0.91428 0.00609 0.06479 0.97467 0.82122 0.49508 0.49851 150 151 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2018-09-26 Hatching Embryo Embryo Imprecise All anatomical structures
49412 49412 SRR7904996 SRX4741349 SRS3822681 SRP162658 PRJNA493234 Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x] GSE120503 Other To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics. parent bioproject:PRJNA493631 pubmed:31042481;pubmed:33785593   52 hpf CHT cells GSM3402061   tissue:zebrafish embryos|region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf 52 hpf CHT cells UMI tools was used to analysis our single cell data. Firstly in “whitelist” step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts zebrafish embryos   The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture’s introduction.   region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf GSM3402061 GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq GSM3402061   1 The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture's introduction. GEO Accession:GSM3402061 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP162658     171353A_zebrafish_HSC_mixture-4_S12_L002_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-4_S12_L002_R2_001.fastq.gz fastq fastq 23083950792.0 76709058.0 GSM3402061 r8 0:150.50 1:150.43 A:6509221386;C:3683018771;G:3901144866;T:8989732881;N:832888 150 150     6509221386 3683018771 3901144866 8989732881 832888 SRX4741349 SRS3822681 SRA784241 GEO Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB) 2 0.04694 0.91333 0.00703 0.06467 0.97447 0.82268 0.467 0.50114 151 151 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2018-09-26 Hatching Embryo Embryo Imprecise All anatomical structures
50657 50657 SRR8206458 SRX5025783 SRS4057283 SRP169565 PRJNA506002 Unifying Developmental Programs for Embryonic and Post Embryonic Neurogenesis in the Zebrafish Retina GSE122680 Transcriptome Analysis It provides an opportunity to make the first comparative study of molecular programs used by embryonic and post embryonic neurogenic programs in the vertebrate retina. Overall design: Retinal samples from 4 developmental stages and 1 post embryonic stage   pubmed:32467236   14 dpf retina rep GSM3478019   source name:Retina|strain:AB|genotype:wildtype|tissue:CMZ|developmental stage:14 dpf 14 dpf retina rep Single cell FASTQ sequencing reads Novogene aligned to the zebrafish genome Zv10 were processed and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite v2.1.0 provided in 10x genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. To further analyze the data we used an analysis pipeline provided by the Seurat R package http://satijalab.org/seurat/. We substract progenitor cell clusters of 36hpf and 48hpf samples according to the proliferative gene expression. For post embryonic samples we substract the ciliary marginal zone CMZ cell clusters based on marker genes' expression. Genome build: Zv10 Supplementary files format and content: barcodes.tsv genes.tsv matrix.mtx Retina   We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40μm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer’s protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer’s protocol.   strain:AB|genotype:wildtype|tissue:CMZ|developmental stage:14 dpf GSM3478019 GSM3478019: 14 dpf retina rep; Danio rerio; RNA Seq GSM3478019   1 We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40μm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer's protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer's protocol. GEO Accession:GSM3478019 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP169565     14dpf_rep_possorted_genome_bam.bam 10X Genomics bam file 47036574600.0 313577164.0 GSM3478019 r1 0:150 A:13973403132;C:10042891919;G:11111376691;T:11908672715;N:230143 150       13973403132 10042891919 11111376691 11908672715 230143 SRX5025783 SRS4057283 SRA812747 GEO Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS 1 0.93407   0.06456   0.84522   0.48431   150   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2018-11-19 Larval Larval Embryo Imprecise All anatomical structures
50659 50659 SRR11812065 SRX5025781 SRS4057281 SRP169565 PRJNA506002 Unifying Developmental Programs for Embryonic and Post Embryonic Neurogenesis in the Zebrafish Retina GSE122680 Transcriptome Analysis It provides an opportunity to make the first comparative study of molecular programs used by embryonic and post embryonic neurogenic programs in the vertebrate retina. Overall design: Retinal samples from 4 developmental stages and 1 post embryonic stage   pubmed:32467236   14 dpf retina GSM3478017   source name:Retina|strain:AB|genotype:wildtype|tissue:CMZ|developmental stage:14 dpf 14 dpf retina Single cell FASTQ sequencing reads Novogene aligned to the zebrafish genome Zv10 were processed and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite v2.1.0 provided in 10x genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. To further analyze the data we used an analysis pipeline provided by the Seurat R package http://satijalab.org/seurat/. We substract progenitor cell clusters of 36hpf and 48hpf samples according to the proliferative gene expression. For post embryonic samples we substract the ciliary marginal zone CMZ cell clusters based on marker genes' expression. Genome build: Zv10 Supplementary files format and content: barcodes.tsv genes.tsv matrix.mtx Retina   We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40μm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer’s protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer’s protocol.   strain:AB|genotype:wildtype|tissue:CMZ|developmental stage:14 dpf GSM3478017 GSM3478017: 14 dpf retina; Danio rerio; RNA Seq GSM3478017   1 We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40μm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer's protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer's protocol. GEO Accession:GSM3478017 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP169565   intentional duplicate 14dpf_possorted_genome_bam.bam 10X Genomics bam file 49517321418.0 342283822.0 GSM3478017 r11 0:144.67 A:14667671784;C:10143561921;G:11341438449;T:13364496000;N:153264 144       14667671784 10143561921 11341438449 13364496000 153264 SRX5025781 SRS4057281 SRA812747 GEO Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS 1 0.88653   0.0963   0.81909   0.51027   150   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2018-11-19 Larval Larval Embryo Imprecise All anatomical structures
51192 51192 SRR8592248 SRX5392461 SRS4380284 SRP186305 PRJNA522917 Pbx4 limits vertebrate heart size and promotes pharyngeal arch artery development through partitioning progenitor fates within the second heart field and restricting proliferation GSE126647 Transcriptome Analysis Development of the vertebrate heart requires the appropriate integration of temporally distinct differentiating progenitor populations. While factors that promote accrual of later differentiating second heart field SHF derived cells to the outflow tract OFT have been intensively investigated few signals are understood that specifically restrict the size of the vertebrate OFT. Here we show that improper specification and proliferation of SHF progenitors in zebrafish lazarus lzr mutants which lack the transcription factor Pbx4 produces enlarged hearts with a specific increase in ventricular cardiomyocytes and smooth muscle cells within the OFT. Specifically optogenetic lineage tracing demonstrates Pbx4 initially promotes the proper partitioning of the SHF into anterior progenitors which contribute to the OFT and adjacent endothelial cell progenitors which contribute to posterior pharyngeal arch arteries. Subsequently Pbx4 also limits the size of the SHF through repressing SHF progenitor proliferation. Single cell RNA sequencing of nkx2.5+ cells revealed that the enlarged SHF progenitor population within Pbx4 deficient embryos assimilates characteristics of normally distinct proliferative and more anterior differentiated cardiomyocyte populations. Therefore the generation of proper OFT size and great arteries in vertebrates requires Pbx dependent stratification of unique progenitor differentiation states to facilitate homeotic like transformations and limit progenitor production within the SHF. Overall design: To determine the effects of Pbx4 loss on cardiac progenitors and differentiated cardiomyocytes we utilized single cell RNA Seq scRNA Seq data sets collected from control and Pbx4 depleted embryos nkx2.5:ZsYellow+ cells at 28 hours post ferlilization. The 10x Genomics platform was used for these studies version 2 library chemistry.   pubmed:32094112   control nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq GSM3610370   tissue:control nkx2.5:ZsYellow+ cells|strain background:AB/TU|age:28 hpf progenitors and cardiomyocytes|cell type:nkx2.5:ZsYellow+ cells control nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq Illumina HiSeq2500 used for basecalling CellRanger software package used for alignment filtering barcode reading prior to post processing with ICGS in AltAnalyze. Genome build: GRCz10/danRer10 Supplementary files format and content: 10X Genomics Chromium Raw Gene BC Cellular Barcodes barcode.tsv Genes genes.tsv and Matrix matrix.mtx control nkx2.5:ZsYellow+ cells   Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver 2016 with the following modifications approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank’s Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down first with a p1000 tip and subsequently with a p100 tip as described by Samsa et al. 2016. Following yolk removal embryos were incubated at 32.5°C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al. 2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry   strain background:AB/TU|age:28 hpf progenitors and cardiomyocytes|cell type:nkx2.5:ZsYellow+ cells GSM3610370 GSM3610370: control nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq; Danio rerio; RNA Seq GSM3610370   1 Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver 2016 with the following modifications approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank's Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down first with a p1000 tip and subsequently with a p100 tip as described by Samsa et al. 2016. Following yolk removal embryos were incubated at 32.5°C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al. 2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry GEO Accession:GSM3610370 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP186305   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=10X Ctrl uninjected 3zf S1 L001 I1 001.fastq.gz read2PairFiles=10X Ctrl uninjected 3zf S1 L001 R1 001.fastq.gz read3PairFiles=10X Ctrl uninjected 3zf S1 L001 R2 001.fastq.gz 10X_Ctrl_uninjected_3zf_S1_L001_I1_001.fastq.gz 10X_Ctrl_uninjected_3zf_S1_L001_R1_001.fastq.gz 10X_Ctrl_uninjected_3zf_S1_L001_R2_001.fastq.gz fastq fastq fastq 13724509526.0 75409393.0 GSM3610370 r1 0:8 1:27 2:147 A:3850897681;C:3014748648;G:3154637947;T:3685016570;N:19208680 8 27 147   3850897681 3014748648 3154637947 3685016570 19208680 SRX5392461 SRS4380284 SRA850447 GEO Nathan Salomonis, Biomedical Informatics, Cincinnati Children's Hospital 1 0.91575   0.07488   0.82871   0.51761   147   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-02-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
51193 51193 SRR8592249 SRX5392461 SRS4380284 SRP186305 PRJNA522917 Pbx4 limits vertebrate heart size and promotes pharyngeal arch artery development through partitioning progenitor fates within the second heart field and restricting proliferation GSE126647 Transcriptome Analysis Development of the vertebrate heart requires the appropriate integration of temporally distinct differentiating progenitor populations. While factors that promote accrual of later differentiating second heart field SHF derived cells to the outflow tract OFT have been intensively investigated few signals are understood that specifically restrict the size of the vertebrate OFT. Here we show that improper specification and proliferation of SHF progenitors in zebrafish lazarus lzr mutants which lack the transcription factor Pbx4 produces enlarged hearts with a specific increase in ventricular cardiomyocytes and smooth muscle cells within the OFT. Specifically optogenetic lineage tracing demonstrates Pbx4 initially promotes the proper partitioning of the SHF into anterior progenitors which contribute to the OFT and adjacent endothelial cell progenitors which contribute to posterior pharyngeal arch arteries. Subsequently Pbx4 also limits the size of the SHF through repressing SHF progenitor proliferation. Single cell RNA sequencing of nkx2.5+ cells revealed that the enlarged SHF progenitor population within Pbx4 deficient embryos assimilates characteristics of normally distinct proliferative and more anterior differentiated cardiomyocyte populations. Therefore the generation of proper OFT size and great arteries in vertebrates requires Pbx dependent stratification of unique progenitor differentiation states to facilitate homeotic like transformations and limit progenitor production within the SHF. Overall design: To determine the effects of Pbx4 loss on cardiac progenitors and differentiated cardiomyocytes we utilized single cell RNA Seq scRNA Seq data sets collected from control and Pbx4 depleted embryos nkx2.5:ZsYellow+ cells at 28 hours post ferlilization. The 10x Genomics platform was used for these studies version 2 library chemistry.   pubmed:32094112   control nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq GSM3610370   tissue:control nkx2.5:ZsYellow+ cells|strain background:AB/TU|age:28 hpf progenitors and cardiomyocytes|cell type:nkx2.5:ZsYellow+ cells control nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq Illumina HiSeq2500 used for basecalling CellRanger software package used for alignment filtering barcode reading prior to post processing with ICGS in AltAnalyze. Genome build: GRCz10/danRer10 Supplementary files format and content: 10X Genomics Chromium Raw Gene BC Cellular Barcodes barcode.tsv Genes genes.tsv and Matrix matrix.mtx control nkx2.5:ZsYellow+ cells   Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver 2016 with the following modifications approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank’s Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down first with a p1000 tip and subsequently with a p100 tip as described by Samsa et al. 2016. Following yolk removal embryos were incubated at 32.5°C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al. 2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry   strain background:AB/TU|age:28 hpf progenitors and cardiomyocytes|cell type:nkx2.5:ZsYellow+ cells GSM3610370 GSM3610370: control nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq; Danio rerio; RNA Seq GSM3610370   1 Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver 2016 with the following modifications approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank's Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down first with a p1000 tip and subsequently with a p100 tip as described by Samsa et al. 2016. Following yolk removal embryos were incubated at 32.5°C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al. 2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry GEO Accession:GSM3610370 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP186305   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=10X Ctrl uninjected 3zf S1 L002 I1 001.fastq.gz read2PairFiles=10X Ctrl uninjected 3zf S1 L002 R1 001.fastq.gz read3PairFiles=10X Ctrl uninjected 3zf S1 L002 R2 001.fastq.gz 10X_Ctrl_uninjected_3zf_S1_L002_I1_001.fastq.gz 10X_Ctrl_uninjected_3zf_S1_L002_R1_001.fastq.gz 10X_Ctrl_uninjected_3zf_S1_L002_R2_001.fastq.gz fastq fastq fastq 13903413706.0 76392383.0 GSM3610370 r2 0:8 1:27 2:147 A:3900618364;C:3054470646;G:3195816893;T:3735199844;N:17307959 8 27 147   3900618364 3054470646 3195816893 3735199844 17307959 SRX5392461 SRS4380284 SRA850447 GEO Nathan Salomonis, Biomedical Informatics, Cincinnati Children's Hospital 1 0.91438   0.07364   0.82893   0.50278   147   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-02-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
55649 55649 SRR10611686 SRX7290958 SRS5784121 SRP235262 PRJNA594336 Single cell sequencing reveals heterogeneity effects of bisphenol A on zebrafish embryonic development GSE141664 Transcriptome Analysis Embryonic period is sensitive window of bisphenol A BPA exposure. However embryonic development is a highly dynamic process with changing cell populations and gene expression profiles. Heterogeneity effects of BPA on fish embryonic development remain not clear. This study applied single cell RNA sequencing to analyze the impact of BPA exposure on transcriptome heterogeneity of 64683 cells from zebrafish embryos at 8 12 hpf and 30 hpf. A total of 38 cell populations were identified and gene expression profiles of 16 cell populations were significantly altered by BPA exposure. The strongest toxic effects of BPA were found at 12 hpf of segmentation stage which is an active stage of cell differentiation. At 8 hpf BPA mainly influenced the outer layer cell populations of embryos such as neural plate border and enveloping layer cells. At 12 hpf and 30 hpf nervous system formation and heart morphogenesis were disturbed. Differential process of neural plate border neural crest and neuron cells was altered leading to increased neurogenesis. For the forebrain midbrain neurons and optic cells the altered cell division and DNA replication and repair were identified. Our study for the first time provides the comprehensive understanding of BPA toxicity on fish embryo development at single cell levels. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish embryonic development following exposure to bisphenol A at different stage gastrulation segmentation and pharyngula.       BP 30h GSM4210785   source name:zebrafish embryo|tissue:embryonic single cell suspension|age:30hpf|exposed pollutants:100ppb BPA BP 30h We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip… zebrafish embryo Exposure solutions were prepared by adding 100 μg/L BPA to culture medium. The exposure solution were was replaced every 12 hours.At three different stages gasturla  segmentation and pharyngula zebrafish embryo were collected. The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an illumina Xten.   tissue:embryonic single cell suspension|age:30hpf|exposed pollutants:100ppb BPA GSM4210785 GSM4210785: BP 30h; Danio rerio; RNA Seq GSM4210785   1 The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an illumina Xten. GEO Accession:GSM4210785 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP235262     BP-30h_S6_L006_R1_001.fastq.gz BP-30h_S6_L006_R2_001.fastq.gz fastq fastq 123297367860.0 408269430.0 GSM4210785 r1 0:151 1:151 A:29612865612;C:21327621660;G:21810738134;T:50523353893;N:22788561 151 151     29612865612 21327621660 21810738134 50523353893 22788561 SRX7290958 SRS5784121 SRA1008496 GEO Nanjing University 2 0.07493 0.92162 0.00891 0.06219 0.98299 0.81594 0.48492 0.48154 151 151 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2019-12-09 Pharyngula Embryo Embryo Imprecise All anatomical structures
55650 55650 SRR10611685 SRX7290957 SRS5784120 SRP235262 PRJNA594336 Single cell sequencing reveals heterogeneity effects of bisphenol A on zebrafish embryonic development GSE141664 Transcriptome Analysis Embryonic period is sensitive window of bisphenol A BPA exposure. However embryonic development is a highly dynamic process with changing cell populations and gene expression profiles. Heterogeneity effects of BPA on fish embryonic development remain not clear. This study applied single cell RNA sequencing to analyze the impact of BPA exposure on transcriptome heterogeneity of 64683 cells from zebrafish embryos at 8 12 hpf and 30 hpf. A total of 38 cell populations were identified and gene expression profiles of 16 cell populations were significantly altered by BPA exposure. The strongest toxic effects of BPA were found at 12 hpf of segmentation stage which is an active stage of cell differentiation. At 8 hpf BPA mainly influenced the outer layer cell populations of embryos such as neural plate border and enveloping layer cells. At 12 hpf and 30 hpf nervous system formation and heart morphogenesis were disturbed. Differential process of neural plate border neural crest and neuron cells was altered leading to increased neurogenesis. For the forebrain midbrain neurons and optic cells the altered cell division and DNA replication and repair were identified. Our study for the first time provides the comprehensive understanding of BPA toxicity on fish embryo development at single cell levels. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish embryonic development following exposure to bisphenol A at different stage gastrulation segmentation and pharyngula.       BP 12h GSM4210784   source name:zebrafish embryo|tissue:embryonic single cell suspension|age:12hpf|exposed pollutants:100ppb BPA BP 12h We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip… zebrafish embryo Exposure solutions were prepared by adding 100 μg/L BPA to culture medium. The exposure solution were was replaced every 12 hours.At three different stages gasturla  segmentation and pharyngula zebrafish embryo were collected. The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an illumina Xten.   tissue:embryonic single cell suspension|age:12hpf|exposed pollutants:100ppb BPA GSM4210784 GSM4210784: BP 12h; Danio rerio; RNA Seq GSM4210784   1 The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an illumina Xten. GEO Accession:GSM4210784 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP235262     BP-12h_S4_L004_R1_001.fastq.gz BP-12h_S4_L004_R2_001.fastq.gz fastq fastq 107141069708.0 354771754.0 GSM4210784 r1 0:151 1:151 A:26617621707;C:17860363455;G:18438338656;T:44205389572;N:19356318 151 151     26617621707 17860363455 18438338656 44205389572 19356318 SRX7290957 SRS5784120 SRA1008496 GEO Nanjing University 2 0.08704 0.91488 0.01108 0.08743 0.98494 0.81316 0.53016 0.47931 151 151 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2019-12-09 Segmentation Embryo Embryo Imprecise All anatomical structures
55651 55651 SRR10611684 SRX7290956 SRS5784117 SRP235262 PRJNA594336 Single cell sequencing reveals heterogeneity effects of bisphenol A on zebrafish embryonic development GSE141664 Transcriptome Analysis Embryonic period is sensitive window of bisphenol A BPA exposure. However embryonic development is a highly dynamic process with changing cell populations and gene expression profiles. Heterogeneity effects of BPA on fish embryonic development remain not clear. This study applied single cell RNA sequencing to analyze the impact of BPA exposure on transcriptome heterogeneity of 64683 cells from zebrafish embryos at 8 12 hpf and 30 hpf. A total of 38 cell populations were identified and gene expression profiles of 16 cell populations were significantly altered by BPA exposure. The strongest toxic effects of BPA were found at 12 hpf of segmentation stage which is an active stage of cell differentiation. At 8 hpf BPA mainly influenced the outer layer cell populations of embryos such as neural plate border and enveloping layer cells. At 12 hpf and 30 hpf nervous system formation and heart morphogenesis were disturbed. Differential process of neural plate border neural crest and neuron cells was altered leading to increased neurogenesis. For the forebrain midbrain neurons and optic cells the altered cell division and DNA replication and repair were identified. Our study for the first time provides the comprehensive understanding of BPA toxicity on fish embryo development at single cell levels. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish embryonic development following exposure to bisphenol A at different stage gastrulation segmentation and pharyngula.       BP 8h GSM4210783   source name:zebrafish embryo|tissue:embryonic single cell suspension|age:8hpf|exposed pollutants:100ppb BPA BP 8h We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip… zebrafish embryo Exposure solutions were prepared by adding 100 μg/L BPA to culture medium. The exposure solution were was replaced every 12 hours.At three different stages gasturla  segmentation and pharyngula zebrafish embryo were collected. The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an illumina Xten.   tissue:embryonic single cell suspension|age:8hpf|exposed pollutants:100ppb BPA GSM4210783 GSM4210783: BP 8h; Danio rerio; RNA Seq GSM4210783   1 The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an illumina Xten. GEO Accession:GSM4210783 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP235262     BP-8h_S2_L002_R1_001.fastq.gz BP-8h_S2_L002_R2_001.fastq.gz fastq fastq 112920017284.0 373907342.0 GSM4210783 r1 0:151 1:151 A:29091217868;C:18813523727;G:19294526701;T:45706210539;N:14538449 151 151     29091217868 18813523727 19294526701 45706210539 14538449 SRX7290956 SRS5784117 SRA1008496 GEO Nanjing University 2 0.13456 0.90846 0.01758 0.09803 0.98293 0.81826 0.55099 0.50254 151 151 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2019-12-09 Gastrula Embryo Embryo Imprecise All anatomical structures
55652 55652 SRR10611683 SRX7290955 SRS5784116 SRP235262 PRJNA594336 Single cell sequencing reveals heterogeneity effects of bisphenol A on zebrafish embryonic development GSE141664 Transcriptome Analysis Embryonic period is sensitive window of bisphenol A BPA exposure. However embryonic development is a highly dynamic process with changing cell populations and gene expression profiles. Heterogeneity effects of BPA on fish embryonic development remain not clear. This study applied single cell RNA sequencing to analyze the impact of BPA exposure on transcriptome heterogeneity of 64683 cells from zebrafish embryos at 8 12 hpf and 30 hpf. A total of 38 cell populations were identified and gene expression profiles of 16 cell populations were significantly altered by BPA exposure. The strongest toxic effects of BPA were found at 12 hpf of segmentation stage which is an active stage of cell differentiation. At 8 hpf BPA mainly influenced the outer layer cell populations of embryos such as neural plate border and enveloping layer cells. At 12 hpf and 30 hpf nervous system formation and heart morphogenesis were disturbed. Differential process of neural plate border neural crest and neuron cells was altered leading to increased neurogenesis. For the forebrain midbrain neurons and optic cells the altered cell division and DNA replication and repair were identified. Our study for the first time provides the comprehensive understanding of BPA toxicity on fish embryo development at single cell levels. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish embryonic development following exposure to bisphenol A at different stage gastrulation segmentation and pharyngula.       CK 30h GSM4210782   source name:zebrafish embryo|tissue:embryonic single cell suspension|age:30hpf|exposed pollutants:n1 CK 30h We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip… zebrafish embryo Exposure solutions were prepared by adding 100 μg/L BPA to culture medium. The exposure solution were was replaced every 12 hours.At three different stages gasturla  segmentation and pharyngula zebrafish embryo were collected. The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an illumina Xten.   tissue:embryonic single cell suspension|age:30hpf|exposed pollutants:n1 GSM4210782 GSM4210782: CK 30h; Danio rerio; RNA Seq GSM4210782   1 The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an illumina Xten. GEO Accession:GSM4210782 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP235262     CK-30h_S5_L005_R1_001.fastq.gz CK-30h_S5_L005_R2_001.fastq.gz fastq fastq 106224273812.0 351736006.0 GSM4210782 r1 0:151 1:151 A:25405444654;C:18089775514;G:18594095209;T:44115027002;N:19931433 151 151     25405444654 18089775514 18594095209 44115027002 19931433 SRX7290955 SRS5784116 SRA1008496 GEO Nanjing University 2 0.06113 0.92264 0.00743 0.0605 0.98415 0.81675 0.50316 0.47382 151 151 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2019-12-09 Pharyngula Embryo Embryo Imprecise All anatomical structures
55653 55653 SRR10611682 SRX7290954 SRS5784119 SRP235262 PRJNA594336 Single cell sequencing reveals heterogeneity effects of bisphenol A on zebrafish embryonic development GSE141664 Transcriptome Analysis Embryonic period is sensitive window of bisphenol A BPA exposure. However embryonic development is a highly dynamic process with changing cell populations and gene expression profiles. Heterogeneity effects of BPA on fish embryonic development remain not clear. This study applied single cell RNA sequencing to analyze the impact of BPA exposure on transcriptome heterogeneity of 64683 cells from zebrafish embryos at 8 12 hpf and 30 hpf. A total of 38 cell populations were identified and gene expression profiles of 16 cell populations were significantly altered by BPA exposure. The strongest toxic effects of BPA were found at 12 hpf of segmentation stage which is an active stage of cell differentiation. At 8 hpf BPA mainly influenced the outer layer cell populations of embryos such as neural plate border and enveloping layer cells. At 12 hpf and 30 hpf nervous system formation and heart morphogenesis were disturbed. Differential process of neural plate border neural crest and neuron cells was altered leading to increased neurogenesis. For the forebrain midbrain neurons and optic cells the altered cell division and DNA replication and repair were identified. Our study for the first time provides the comprehensive understanding of BPA toxicity on fish embryo development at single cell levels. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish embryonic development following exposure to bisphenol A at different stage gastrulation segmentation and pharyngula.       CK 12h GSM4210781   source name:zebrafish embryo|tissue:embryonic single cell suspension|age:12hpf|exposed pollutants:n1 CK 12h We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip… zebrafish embryo Exposure solutions were prepared by adding 100 μg/L BPA to culture medium. The exposure solution were was replaced every 12 hours.At three different stages gasturla  segmentation and pharyngula zebrafish embryo were collected. The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an illumina Xten.   tissue:embryonic single cell suspension|age:12hpf|exposed pollutants:n1 GSM4210781 GSM4210781: CK 12h; Danio rerio; RNA Seq GSM4210781   1 The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an illumina Xten. GEO Accession:GSM4210781 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP235262     CK-12h_S3_L003_R1_001.fastq.gz CK-12h_S3_L003_R2_001.fastq.gz fastq fastq 104307666146.0 345389623.0 GSM4210781 r1 0:151 1:151 A:25979928759;C:17362219827;G:18048535744;T:42903273069;N:13708747 151 151     25979928759 17362219827 18048535744 42903273069 13708747 SRX7290954 SRS5784119 SRA1008496 GEO Nanjing University 2 0.08003 0.91078 0.01149 0.08744 0.98561 0.81152 0.53825 0.48534 151 151 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2019-12-09 Segmentation Embryo Embryo Imprecise All anatomical structures
55654 55654 SRR10611681 SRX7290953 SRS5784118 SRP235262 PRJNA594336 Single cell sequencing reveals heterogeneity effects of bisphenol A on zebrafish embryonic development GSE141664 Transcriptome Analysis Embryonic period is sensitive window of bisphenol A BPA exposure. However embryonic development is a highly dynamic process with changing cell populations and gene expression profiles. Heterogeneity effects of BPA on fish embryonic development remain not clear. This study applied single cell RNA sequencing to analyze the impact of BPA exposure on transcriptome heterogeneity of 64683 cells from zebrafish embryos at 8 12 hpf and 30 hpf. A total of 38 cell populations were identified and gene expression profiles of 16 cell populations were significantly altered by BPA exposure. The strongest toxic effects of BPA were found at 12 hpf of segmentation stage which is an active stage of cell differentiation. At 8 hpf BPA mainly influenced the outer layer cell populations of embryos such as neural plate border and enveloping layer cells. At 12 hpf and 30 hpf nervous system formation and heart morphogenesis were disturbed. Differential process of neural plate border neural crest and neuron cells was altered leading to increased neurogenesis. For the forebrain midbrain neurons and optic cells the altered cell division and DNA replication and repair were identified. Our study for the first time provides the comprehensive understanding of BPA toxicity on fish embryo development at single cell levels. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish embryonic development following exposure to bisphenol A at different stage gastrulation segmentation and pharyngula.       CK 8h GSM4210780   source name:zebrafish embryo|tissue:embryonic single cell suspension|age:8hpf|exposed pollutants:n1 CK 8h We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip… zebrafish embryo Exposure solutions were prepared by adding 100 μg/L BPA to culture medium. The exposure solution were was replaced every 12 hours.At three different stages gasturla  segmentation and pharyngula zebrafish embryo were collected. The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an illumina Xten.   tissue:embryonic single cell suspension|age:8hpf|exposed pollutants:n1 GSM4210780 GSM4210780: CK 8h; Danio rerio; RNA Seq GSM4210780   1 The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an illumina Xten. GEO Accession:GSM4210780 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP235262     CK-8h_S1_L001_R1_001.fastq.gz CK-8h_S1_L001_R2_001.fastq.gz fastq fastq 117112087438.0 387788369.0 GSM4210780 r1 0:151 1:151 A:30237691607;C:19643608086;G:20051803632;T:47157015762;N:21968351 151 151     30237691607 19643608086 20051803632 47157015762 21968351 SRX7290953 SRS5784118 SRA1008496 GEO Nanjing University 2 0.12513 0.90183 0.01627 0.09322 0.98255 0.81937 0.56652 0.49202 151 151 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2019-12-09 Gastrula Embryo Embryo Imprecise All anatomical structures
56746 56746 SRR15813443 SRX12105547 SRS10085839 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   wt s6 GSM5567817   tissue:wt reference hpf 10|strain:WT|Stage:10 hpf|experiment:WT embryo wt s6 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz wt reference hpf 10   10x Genomcis Chromium single cell preparation   strain:WT|Stage:10 hpf|experiment:WT embryo GSM5567817 GSM5567817: wt s6; Danio rerio; RNA Seq GSM5567817   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567817 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate wt_s6_possorted_genome_bam.bam 10X Genomics bam file 10559763630.0 117330707.0 GSM5567817 r1 0:90 A:3140440043;C:2269672250;G:2444938588;T:2701186457;N:3526292 90       3140440043 2269672250 2444938588 2701186457 3526292 SRX12105547 SRS10085839 SRA1042742 GEO Washington University in St Louis 1 0.91901   0.24752   0.80736   0.6329   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56747 56747 SRR15813442 SRX12105546 SRS10085840 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   wt s5 GSM5567816   tissue:wt reference hpf 10|strain:WT|Stage:10 hpf|experiment:WT embryo wt s5 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz wt reference hpf 10   10x Genomcis Chromium single cell preparation   strain:WT|Stage:10 hpf|experiment:WT embryo GSM5567816 GSM5567816: wt s5; Danio rerio; RNA Seq GSM5567816   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567816 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate wt_s5_possorted_genome_bam.bam 10X Genomics bam file 7404734700.0 82274830.0 GSM5567816 r1 0:90 A:2195721377;C:1607643736;G:1735950843;T:1863072717;N:2346027 90       2195721377 1607643736 1735950843 1863072717 2346027 SRX12105546 SRS10085840 SRA1042742 GEO Washington University in St Louis 1 0.91448   0.23763   0.80933   0.63338   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56748 56748 SRR15813441 SRX12105545 SRS10085841 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   wt s4 GSM5567815   tissue:wt reference hpf 8|strain:WT|Stage:8 hpf|experiment:WT embryo wt s4 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz wt reference hpf 8   10x Genomcis Chromium single cell preparation   strain:WT|Stage:8 hpf|experiment:WT embryo GSM5567815 GSM5567815: wt s4; Danio rerio; RNA Seq GSM5567815   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567815 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate wt_s4_possorted_genome_bam.bam 10X Genomics bam file 16164581310.0 179606459.0 GSM5567815 r1 0:90 A:4832582846;C:3490996022;G:3746675672;T:4088577265;N:5749505 90       4832582846 3490996022 3746675672 4088577265 5749505 SRX12105545 SRS10085841 SRA1042742 GEO Washington University in St Louis 1 0.90609   0.22195   0.82085   0.64383   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56749 56749 SRR15813440 SRX12105544 SRS10085838 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   wt s3 GSM5567814   tissue:wt reference hpf 8|strain:WT|Stage:8 hpf|experiment:WT embryo wt s3 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz wt reference hpf 8   10x Genomcis Chromium single cell preparation   strain:WT|Stage:8 hpf|experiment:WT embryo GSM5567814 GSM5567814: wt s3; Danio rerio; RNA Seq GSM5567814   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567814 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate wt_s3_possorted_genome_bam.bam 10X Genomics bam file 13357030950.0 148411455.0 GSM5567814 r1 0:90 A:3992336370;C:2912423812;G:3128958676;T:3318661163;N:4650929 90       3992336370 2912423812 3128958676 3318661163 4650929 SRX12105544 SRS10085838 SRA1042742 GEO Washington University in St Louis 1 0.9059   0.21809   0.82578   0.64796   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56750 56750 SRR15813439 SRX12105543 SRS10085837 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   wt s2 GSM5567813   tissue:wt reference hpf 6|strain:WT|Stage:6 hpf|experiment:WT embryo wt s2 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz wt reference hpf 6   10x Genomcis Chromium single cell preparation   strain:WT|Stage:6 hpf|experiment:WT embryo GSM5567813 GSM5567813: wt s2; Danio rerio; RNA Seq GSM5567813   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567813 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate wt_s2_possorted_genome_bam.bam 10X Genomics bam file 16886072430.0 187623027.0 GSM5567813 r1 0:90 A:4987160925;C:3716401392;G:4001055160;T:4174238739;N:7216214 90       4987160925 3716401392 4001055160 4174238739 7216214 SRX12105543 SRS10085837 SRA1042742 GEO Washington University in St Louis 1 0.9034   0.19315   0.81038   0.65382   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56751 56751 SRR15813438 SRX12105542 SRS10085835 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   wt s1 GSM5567812   tissue:wt reference hpf 6|strain:WT|Stage:6 hpf|experiment:WT embryo wt s1 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz wt reference hpf 6   10x Genomcis Chromium single cell preparation   strain:WT|Stage:6 hpf|experiment:WT embryo GSM5567812 GSM5567812: wt s1; Danio rerio; RNA Seq GSM5567812   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567812 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate wt_s1_possorted_genome_bam.bam 10X Genomics bam file 19790815230.0 219897947.0 GSM5567812 r1 0:90 A:5848816040;C:4330412374;G:4675552886;T:4927327121;N:8706809 90       5848816040 4330412374 4675552886 4927327121 8706809 SRX12105542 SRS10085835 SRA1042742 GEO Washington University in St Louis 1 0.90894   0.18849   0.80771   0.64881   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56752 56752 SRR15813437 SRX12105541 SRS10085836 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   tyr 7 GSM5567811   tissue:tyr crispant|strain:tyr crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo tyr 7 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz tyr crispant   10x Genomcis Chromium single cell preparation   strain:tyr crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567811 GSM5567811: tyr 7; Danio rerio; RNA Seq GSM5567811   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567811 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate tyr_7_possorted_genome_bam.bam 10X Genomics bam file 17956913490.0 199521261.0 GSM5567811 r1 0:90 A:5196658241;C:3876984519;G:4299586871;T:4578633727;N:5050132 90       5196658241 3876984519 4299586871 4578633727 5050132 SRX12105541 SRS10085836 SRA1042742 GEO Washington University in St Louis 1 0.91768   0.22887   0.82108   0.56033   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56753 56753 SRR15813436 SRX12105540 SRS10085834 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   tyr 6 GSM5567810   tissue:tyr crispant|strain:tyr crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo tyr 6 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz tyr crispant   10x Genomcis Chromium single cell preparation   strain:tyr crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567810 GSM5567810: tyr 6; Danio rerio; RNA Seq GSM5567810   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567810 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate tyr_6_possorted_genome_bam.bam 10X Genomics bam file 20779298370.0 230881093.0 GSM5567810 r1 0:90 A:5921943503;C:4559349693;G:5076139988;T:5215980107;N:5885079 90       5921943503 4559349693 5076139988 5215980107 5885079 SRX12105540 SRS10085834 SRA1042742 GEO Washington University in St Louis 1 0.92027   0.21718   0.82558   0.55659   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56754 56754 SRR15813435 SRX12105539 SRS10085833 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   tyr 5 GSM5567809   tissue:tyr crispant|strain:tyr crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo tyr 5 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz tyr crispant   10x Genomcis Chromium single cell preparation   strain:tyr crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567809 GSM5567809: tyr 5; Danio rerio; RNA Seq GSM5567809   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567809 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate tyr_5_possorted_genome_bam.bam 10X Genomics bam file 11100581280.0 123339792.0 GSM5567809 r1 0:90 A:3139119132;C:2435865589;G:2721973969;T:2802951898;N:670692 90       3139119132 2435865589 2721973969 2802951898 670692 SRX12105539 SRS10085833 SRA1042742 GEO Washington University in St Louis 1 0.93417   0.15847   0.83347   0.5442   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56755 56755 SRR15813434 SRX12105538 SRS10085832 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   tyr 4 GSM5567808   tissue:tyr crispant|strain:tyr crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo tyr 4 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz tyr crispant   10x Genomcis Chromium single cell preparation   strain:tyr crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567808 GSM5567808: tyr 4; Danio rerio; RNA Seq GSM5567808   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567808 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate tyr_4_possorted_genome_bam.bam 10X Genomics bam file 12537663570.0 139307373.0 GSM5567808 r1 0:90 A:3622205893;C:2682389272;G:2969276928;T:3261280923;N:2510554 90       3622205893 2682389272 2969276928 3261280923 2510554 SRX12105538 SRS10085832 SRA1042742 GEO Washington University in St Louis 1 0.93183   0.17593   0.82674   0.54339   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56756 56756 SRR15813433 SRX12105537 SRS10085831 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   tyr 3 GSM5567807   tissue:tyr crispant|strain:tyr crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo tyr 3 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz tyr crispant   10x Genomcis Chromium single cell preparation   strain:tyr crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567807 GSM5567807: tyr 3; Danio rerio; RNA Seq GSM5567807   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567807 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate tyr_3_possorted_genome_bam.bam 10X Genomics bam file 14347674270.0 159418603.0 GSM5567807 r1 0:90 A:4145829296;C:3058277848;G:3413742462;T:3725775591;N:4049073 90       4145829296 3058277848 3413742462 3725775591 4049073 SRX12105537 SRS10085831 SRA1042742 GEO Washington University in St Louis 1 0.92892   0.16288   0.82724   0.52654   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56757 56757 SRR15813432 SRX12105536 SRS10085830 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   tyr 2 GSM5567806   tissue:tyr crispant|strain:tyr crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo tyr 2 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz tyr crispant   10x Genomcis Chromium single cell preparation   strain:tyr crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567806 GSM5567806: tyr 2; Danio rerio; RNA Seq GSM5567806   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567806 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate tyr_2_possorted_genome_bam.bam 10X Genomics bam file 10069177770.0 111879753.0 GSM5567806 r1 0:90 A:2905395164;C:2177772281;G:2406688540;T:2577323490;N:1998295 90       2905395164 2177772281 2406688540 2577323490 1998295 SRX12105536 SRS10085830 SRA1042742 GEO Washington University in St Louis 1 0.92725   0.19411   0.831   0.57759   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56758 56758 SRR15813431 SRX12105535 SRS10085829 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   tyr 1 GSM5567805   tissue:tyr crispant|strain:tyr crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo tyr 1 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz tyr crispant   10x Genomcis Chromium single cell preparation   strain:tyr crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567805 GSM5567805: tyr 1; Danio rerio; RNA Seq GSM5567805   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567805 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate tyr_1_possorted_genome_bam.bam 10X Genomics bam file 13916932740.0 154632586.0 GSM5567805 r1 0:90 A:4011009499;C:3001925064;G:3335796140;T:3563954880;N:4247157 90       4011009499 3001925064 3335796140 3563954880 4247157 SRX12105535 SRS10085829 SRA1042742 GEO Washington University in St Louis 1 0.92833   0.18624   0.82584   0.55384   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56759 56759 SRR15813430 SRX12105534 SRS10085828 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   sebox 3 GSM5567804   tissue:sebox crispant|strain:sebox crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo sebox 3 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz sebox crispant   10x Genomcis Chromium single cell preparation   strain:sebox crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567804 GSM5567804: sebox 3; Danio rerio; RNA Seq GSM5567804   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567804 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate sebox_3_possorted_genome_bam.bam 10X Genomics bam file 15063590430.0 167373227.0 GSM5567804 r1 0:90 A:4342780592;C:3200398068;G:3565351581;T:3953977957;N:1082232 90       4342780592 3200398068 3565351581 3953977957 1082232 SRX12105534 SRS10085828 SRA1042742 GEO Washington University in St Louis 1 0.92955   0.17763   0.82382   0.5348   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56760 56760 SRR15813429 SRX12105533 SRS10085827 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   sebox 2 GSM5567803   tissue:sebox crispant|strain:sebox crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo sebox 2 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz sebox crispant   10x Genomcis Chromium single cell preparation   strain:sebox crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567803 GSM5567803: sebox 2; Danio rerio; RNA Seq GSM5567803   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567803 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate sebox_2_possorted_genome_bam.bam 10X Genomics bam file 10155028230.0 112833647.0 GSM5567803 r1 0:90 A:2847715131;C:2249340222;G:2497174890;T:2560077085;N:720902 90       2847715131 2249340222 2497174890 2560077085 720902 SRX12105533 SRS10085827 SRA1042742 GEO Washington University in St Louis 1 0.9413   0.17155   0.83236   0.5478   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56761 56761 SRR15813428 SRX12105532 SRS10085826 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   sebox 1 GSM5567802   tissue:sebox crispant|strain:sebox crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo sebox 1 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz sebox crispant   10x Genomcis Chromium single cell preparation   strain:sebox crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567802 GSM5567802: sebox 1; Danio rerio; RNA Seq GSM5567802   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567802 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate sebox_1_possorted_genome_bam.bam 10X Genomics bam file 15631632990.0 173684811.0 GSM5567802 r1 0:90 A:4504570341;C:3335848026;G:3720024502;T:4070070942;N:1119179 90       4504570341 3335848026 3720024502 4070070942 1119179 SRX12105532 SRS10085826 SRA1042742 GEO Washington University in St Louis 1 0.91841   0.19   0.82367   0.54474   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56762 56762 SRR15813427 SRX12105531 SRS10085825 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   noto 3 GSM5567801   tissue:noto crispant|strain:noto crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo noto 3 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz noto crispant   10x Genomcis Chromium single cell preparation   strain:noto crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567801 GSM5567801: noto 3; Danio rerio; RNA Seq GSM5567801   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567801 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate noto_3_possorted_genome_bam.bam 10X Genomics bam file 9696476250.0 107738625.0 GSM5567801 r1 0:90 A:2759552091;C:2046867650;G:2381514508;T:2503080064;N:5461937 90       2759552091 2046867650 2381514508 2503080064 5461937 SRX12105531 SRS10085825 SRA1042742 GEO Washington University in St Louis 1 0.88572   0.24263   0.83228   0.5118   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56763 56763 SRR15813426 SRX12105530 SRS10085824 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   noto 2 GSM5567800   tissue:noto crispant|strain:noto crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo noto 2 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz noto crispant   10x Genomcis Chromium single cell preparation   strain:noto crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567800 GSM5567800: noto 2; Danio rerio; RNA Seq GSM5567800   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567800 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate noto_2_possorted_genome_bam.bam 10X Genomics bam file 6805896120.0 75621068.0 GSM5567800 r1 0:90 A:1937849673;C:1444333862;G:1669710397;T:1750230467;N:3771721 90       1937849673 1444333862 1669710397 1750230467 3771721 SRX12105530 SRS10085824 SRA1042742 GEO Washington University in St Louis 1 0.88304   0.22942   0.82958   0.50945   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56764 56764 SRR15813425 SRX12105529 SRS10085822 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   noto 1 GSM5567799   tissue:noto crispant|strain:noto crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo noto 1 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz noto crispant   10x Genomcis Chromium single cell preparation   strain:noto crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567799 GSM5567799: noto 1; Danio rerio; RNA Seq GSM5567799   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567799 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate noto_1_possorted_genome_bam.bam 10X Genomics bam file 7424025120.0 82489168.0 GSM5567799 r1 0:90 A:2111968765;C:1577509540;G:1827370183;T:1903046323;N:4130309 90       2111968765 1577509540 1827370183 1903046323 4130309 SRX12105529 SRS10085822 SRA1042742 GEO Washington University in St Louis 1 0.86603   0.22594   0.83073   0.51508   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56765 56765 SRR15813424 SRX12105528 SRS10085823 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   lhx1a 4 GSM5567798   tissue:lhx1a crispant|strain:lhx1a crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo lhx1a 4 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz lhx1a crispant   10x Genomcis Chromium single cell preparation   strain:lhx1a crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567798 GSM5567798: lhx1a 4; Danio rerio; RNA Seq GSM5567798   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567798 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate lhx1a_4_possorted_genome_bam.bam 10X Genomics bam file 22087787670.0 245419863.0 GSM5567798 r1 0:90 A:6475797345;C:4735192179;G:5275258568;T:5599207862;N:2331716 90       6475797345 4735192179 5275258568 5599207862 2331716 SRX12105528 SRS10085823 SRA1042742 GEO Washington University in St Louis 1 0.91015   0.22744   0.83278   0.55743   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56766 56766 SRR15813423 SRX12105527 SRS10085820 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   lhx1a 3 GSM5567797   tissue:lhx1a crispant|strain:lhx1a crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo lhx1a 3 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz lhx1a crispant   10x Genomcis Chromium single cell preparation   strain:lhx1a crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567797 GSM5567797: lhx1a 3; Danio rerio; RNA Seq GSM5567797   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567797 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate lhx1a_3_possorted_genome_bam.bam 10X Genomics bam file 20620567800.0 229117420.0 GSM5567797 r1 0:90 A:5887591442;C:4508984476;G:5046355704;T:5175484329;N:2151849 90       5887591442 4508984476 5046355704 5175484329 2151849 SRX12105527 SRS10085820 SRA1042742 GEO Washington University in St Louis 1 0.92195   0.22061   0.83224   0.56225   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56767 56767 SRR15813422 SRX12105526 SRS10085821 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   lhx1a 2 GSM5567796   tissue:lhx1a crispant|strain:lhx1a crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo lhx1a 2 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz lhx1a crispant   10x Genomcis Chromium single cell preparation   strain:lhx1a crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567796 GSM5567796: lhx1a 2; Danio rerio; RNA Seq GSM5567796   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567796 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate lhx1a_2_possorted_genome_bam.bam 10X Genomics bam file 9946966230.0 110521847.0 GSM5567796 r1 0:90 A:2788146910;C:2206643231;G:2469755316;T:2481819884;N:600889 90       2788146910 2206643231 2469755316 2481819884 600889 SRX12105526 SRS10085821 SRA1042742 GEO Washington University in St Louis 1 0.91371   0.24403   0.82629   0.58866   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56768 56768 SRR15813421 SRX12105525 SRS10085819 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   lhx1a 1 GSM5567795   tissue:lhx1a crispant|strain:lhx1a crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo lhx1a 1 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz lhx1a crispant   10x Genomcis Chromium single cell preparation   strain:lhx1a crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567795 GSM5567795: lhx1a 1; Danio rerio; RNA Seq GSM5567795   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567795 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate lhx1a_1_possorted_genome_bam.bam 10X Genomics bam file 19493469630.0 216594107.0 GSM5567795 r1 0:90 A:5626093917;C:4175669632;G:4665965196;T:5024562911;N:1177974 90       5626093917 4175669632 4665965196 5024562911 1177974 SRX12105525 SRS10085819 SRA1042742 GEO Washington University in St Louis 1 0.90552   0.2132   0.81921   0.56307   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56769 56769 SRR15813420 SRX12105524 SRS10085818 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   irx3a 3 GSM5567794   tissue:irx3a crispant|strain:irx3a crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo irx3a 3 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz irx3a crispant   10x Genomcis Chromium single cell preparation   strain:irx3a crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567794 GSM5567794: irx3a 3; Danio rerio; RNA Seq GSM5567794   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567794 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate irx3a_3_possorted_genome_bam.bam 10X Genomics bam file 8702629560.0 96695884.0 GSM5567794 r1 0:90 A:2502778147;C:1869454970;G:2100874536;T:2226298889;N:3223018 90       2502778147 1869454970 2100874536 2226298889 3223018 SRX12105524 SRS10085818 SRA1042742 GEO Washington University in St Louis 1 0.93135   0.17699   0.83031   0.56065   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56770 56770 SRR15813419 SRX12105523 SRS10085814 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   irx3a 2 GSM5567793   tissue:irx3a crispant|strain:irx3a crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo irx3a 2 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz irx3a crispant   10x Genomcis Chromium single cell preparation   strain:irx3a crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567793 GSM5567793: irx3a 2; Danio rerio; RNA Seq GSM5567793   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567793 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate irx3a_2_possorted_genome_bam.bam 10X Genomics bam file 13516567200.0 150184080.0 GSM5567793 r1 0:90 A:3934125495;C:2881926208;G:3210954290;T:3485647605;N:3913602 90       3934125495 2881926208 3210954290 3485647605 3913602 SRX12105523 SRS10085814 SRA1042742 GEO Washington University in St Louis 1 0.92263   0.18193   0.8267   0.55492   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
56771 56771 SRR15813418 SRX12105522 SRS10085815 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   irx3a 1 GSM5567792   tissue:irx3a crispant|strain:irx3a crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo irx3a 1 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz irx3a crispant   10x Genomcis Chromium single cell preparation   strain:irx3a crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo GSM5567792 GSM5567792: irx3a 1; Danio rerio; RNA Seq GSM5567792   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567792 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate irx3a_1_possorted_genome_bam.bam 10X Genomics bam file 14095641960.0 156618244.0 GSM5567792 r1 0:90 A:4094793830;C:2977588403;G:3309296706;T:3709972016;N:3991005 90       4094793830 2977588403 3309296706 3709972016 3991005 SRX12105522 SRS10085815 SRA1042742 GEO Washington University in St Louis 1 0.93495   0.16833   0.82505   0.54259   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Embryo Imprecise All anatomical structures
61425 61425 SRR12749598 SRX9221555 SRS7455256 SRP285948 PRJNA666689 Spatio temporal mRNA tracking in the early zebrafish embryo GSE158849 Other We performed spatially resolved transcriptomics with sub single cell resolution in zebrafish embryos at the one cell stage which allowed us to identify a class of mRNAs that is specifically localized at an extraembryonic position in the yolk sac the vegetal pole. The three prime UTRs of these localized genes are enriched in specific sequence motifs. Comparison to two frog species revealed relatively low conservation of localized genes but high conservation of sequence motifs. In vivo RNA labeling followed by scRNA seq revealed that a large number of the localized transcripts are specifically transported to the primordial germ cells. Overall design: Spatial transcriptomic data tomo seq from zebrafish one cell stage embroys mature X. laevis and X. tropicalis oocytes. Single cell metabolic labeling scSLAM seq of zebrafish embryos at 6 hpf.   pubmed:34099733   scSLAM seq replicate 1 GSM4812182   tissue:shield stage embryos 6 hpf|strain:AB wildtype|treatment:4sUTP injected|extraction protocol:Methanol fixed single cell suspension 10x Genomics transcriptome. scSLAM seq replicate 1 zebrafish tomo seq demultiplexing with bcl2fastq v2.18.0.12 mapping with STAR v2.5.3a split counts by section barcode Genome build: GRCz10 release 90 Supplementary files format and content: csv file containing gene counts per section xenopus tomo seq demultiplexing with bcl2fastq v2.18.0.12 mapping with STAR v2.5.3a split counts by section barcode and translate gene identifier to gene names Genome build: X. tropicalis v9.1 genome assembly X.laevis v9.2 genome assembly Supplementary files format and content: csv file containing gene counts per section scSLAM seq zebrafish demultiplexing using cellranger mkfastq v3.0.2 mapping and whitelisting of cells with cellranger v3.0.2 splitting labeled reads >1 T C mutation from unlabeled into separate fastq files submitted to this GEO entry mapping with STARsolo v2.7.0f 0328 single cell analysis in seurat v3.1.2 Genome build: GRCz11 Supplementary files format and content: barcodes.tsv list of barcodes genes.tsv list of genes and matrix.tsv count matrix shield stage embryos 6 hpf   none provided by the submitter   strain:AB wildtype|treatment:4sUTP injected|extraction protocol:Methanol fixed single cell suspension 10x Genomics transcriptome. GSM4812182 GSM4812182: scSLAM seq replicate 1; Danio rerio; RNA Seq GSM4812182   1 none provided by the submitter GEO Accession:GSM4812182 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP285948     scSLAMseq.zebrafish.6hpf.R1.fastq.gz scSLAMseq.zebrafish.6hpf.R2.fastq.gz fastq fastq 18763873688.0 151321562.0 GSM4812182 r1 0:26 1:98 A:5330726187;C:3994611684;G:4055930332;T:5373535151;N:9070334 26 98     5330726187 3994611684 4055930332 5373535151 9070334 SRX9221555 SRS7455256 SRA1136461 GEO Junker, BIMSB, MDC 2 0.00126 0.81459 0.0004 0.05503 0.99717 0.82674 0.52121 0.58038 26 98 T B sc-like readlen illumina hiseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2020-09-30 Gastrula Embryo Embryo Imprecise All anatomical structures
61615 61615 SRR12888601 SRX9353789 SRS7576887 SRP288474 PRJNA671679 Using a Zebrafish Model to Identify Cellular Responses to Uropathogenic E. coli Bacteremia GSE160038 Transcriptome Analysis Urinary tract infections UTIs are the second most common infections encountered in the pediatric population second only to respiratory tract infections. UTIs are also a major cause of morbidity and mortality. UTIs can often ascend causing infection in the upper urinary tract or even progress to bacteremia or urosepsis. Urosepsis accounts for 10 30% of septic shock cases and Uropathogenic E.coli UPEC is responsible for almost 75% of cases. Therefore increased understanding of the effects of urosepsis at the cellular and organ specific level will provide the foundation for improvements in clinical care. Overall design: Two zebrafish cohorts were injected with either sterile saline or UPEC and subjected to scRNA seq. Cell clusters were identified and subjected to RNA velocity analysis. Selected clusters relevant to the innate immune system and bactericidal activity underwent canonical pathway analysis. RNA velocity analysis revealed several key changes in the transcriptional state of UPEC infected cells and pathway analysis provided key information regarding changes in innate immune pathways within the cell clusters.       UPEC injected 5 dpf embryo cells GSM4855812   source name:5 dpf embryo|tissue preparation:Single cell suspension|tissue:embryo|age:5 days|treatment:UPEC UPEC injected 5 dpf embryo cells CellRanger version 3.1 was utilized to process the raw sequence data generated by the sequencer. CellRanger uses bcl2fastq to demultiplex raw base sequence calls generated from the sequencer into sample specific FASTQ files The FASTQ files were then aligned to the zebrafish reference genome Danio rerio.GRCz11 with RNAseq aligner STAR The aligned reads were traced back to individual cells and the gene expression level of individual genes were quantified based on the number of UMIs unique molecular indices detected in each cell.The filtered feature cell barcode matrices generated by CellRanger were used for further analysis. Genome build: GRCz11 3.1.0 Supplementary files format and content: Tab delimited text file containing count matrix for each gene and cell 5 dpf embryo Zebrafish were injected with red fluorescent protein RFP expressing UPEC. post 24 hours the zebrafish were dissociated and then homogenate was placed on a glass slide and evaluated for RFP expression on Keyence BZII microscope. Allowed embryos to mature for 4 dpf dpf in a 28.5°C incubator in egg water filled petri dishes. Embryos were collected via visualization through dissecting microscope and separated into control and experimental groups each containing about 30 embryos. The embryos were anesthetized with tricaine and immobilized in methylcellulose. A mixture of the bacterial solution described above phenol red and PBS was made.The mixture was loaded into microneedle and about 1nl of the mixture was injected into the pericardial cavity of each embryo in the experimental group. The control group was injected with 1nl of phenol red and PBS. The embryos were then incubated for 24 hours at 28.5°C. The embryos were euthanized with tricaine and ice added to egg water. The embryos were then added to methylcellulose and the heads of the embryos were removed using a straight blade sterile scalpel. The remaining portion of the embryos were collected and washed 2x with cold PBS at 700g for 5 min then dissociated with Liberase TL Sigma containing DNAse I Sigma in DMEM using gentleMACS Miltenyi Biotec in C tubes then cells were incubated at 370C for 10 minutes with continuous monitoring. When cell homogenate started to disappear DMEM containing 10% FBS was added to stop the dissociation reaction. Cells were then filtered on 70µm filter and centrifuged at 1500 rpm for 10 min. Cells were counted on hemocytometer then dead cells were removed using dead cell removal microbead Miltenyi Biotec with MS column. Live cells were then centrifuged and resuspended in DPBS without xxx+ or Mg2+ and processed for single cell RNA sequencing on 10x genomics platform. Library preparation was performed usingChromium™ Next GEM Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1.   tissue preparation:Single cell suspension|tissue:embryo|age:5 days|treatment:UPEC GSM4855812 GSM4855812: UPEC injected 5 dpf embryo cells; Danio rerio; RNA Seq GSM4855812   1 The embryos were euthanized with tricaine and ice added to egg water. The embryos were then added to methylcellulose and the heads of the embryos were removed using a straight blade sterile scalpel. The remaining portion of the embryos were collected and washed 2x with cold PBS at 700g for 5 min then dissociated with Liberase TL Sigma containing DNAse I Sigma in DMEM using gentleMACS Miltenyi Biotec in C tubes then cells were incubated at 370C for 10 minutes with continuous monitoring. When cell homogenate started to disappear DMEM containing 10% FBS was added to stop the dissociation reaction. Cells were then filtered on 70µm filter and centrifuged at 1500 rpm for 10 min. Cells were counted on hemocytometer then dead cells were removed using dead cell removal microbead Miltenyi Biotec with MS column. Live cells were then centrifuged and resuspended in DPBS without xxx+ or Mg2+ and processed for single cell RNA sequencing on 10x genomics platform. Library preparation was performed usingChromium™ Next GEM Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1. GEO Accession:GSM4855812 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP288474   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Upec S4 L001 I1 001.fastq.gz read2PairFiles=Upec S4 L001 R1 001.fastq.gz read3PairFiles=Upec S4 L001 R2 001.fastq.gz Upec_S4_L001_I1_001.fastq.gz Upec_S4_L001_R1_001.fastq.gz Upec_S4_L001_R2_001.fastq.gz fastq fastq fastq 30696246075.0 241702725.0 GSM4855812 r1 0:8 1:28 2:91 A:8297484773;C:7271108187;G:7092330543;T:8034542269;N:780303 8 28 91   8297484773 7271108187 7092330543 8034542269 780303 SRX9353789 SRS7576887 SRA1147613 GEO Pediatric Nephrology, Indiana University School of Medicine 1 0.94674   0.11144   0.79107   0.5211   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   India 2020-10-25 Larval Larval Embryo Imprecise All anatomical structures
61616 61616 SRR12888602 SRX9353789 SRS7576887 SRP288474 PRJNA671679 Using a Zebrafish Model to Identify Cellular Responses to Uropathogenic E. coli Bacteremia GSE160038 Transcriptome Analysis Urinary tract infections UTIs are the second most common infections encountered in the pediatric population second only to respiratory tract infections. UTIs are also a major cause of morbidity and mortality. UTIs can often ascend causing infection in the upper urinary tract or even progress to bacteremia or urosepsis. Urosepsis accounts for 10 30% of septic shock cases and Uropathogenic E.coli UPEC is responsible for almost 75% of cases. Therefore increased understanding of the effects of urosepsis at the cellular and organ specific level will provide the foundation for improvements in clinical care. Overall design: Two zebrafish cohorts were injected with either sterile saline or UPEC and subjected to scRNA seq. Cell clusters were identified and subjected to RNA velocity analysis. Selected clusters relevant to the innate immune system and bactericidal activity underwent canonical pathway analysis. RNA velocity analysis revealed several key changes in the transcriptional state of UPEC infected cells and pathway analysis provided key information regarding changes in innate immune pathways within the cell clusters.       UPEC injected 5 dpf embryo cells GSM4855812   source name:5 dpf embryo|tissue preparation:Single cell suspension|tissue:embryo|age:5 days|treatment:UPEC UPEC injected 5 dpf embryo cells CellRanger version 3.1 was utilized to process the raw sequence data generated by the sequencer. CellRanger uses bcl2fastq to demultiplex raw base sequence calls generated from the sequencer into sample specific FASTQ files The FASTQ files were then aligned to the zebrafish reference genome Danio rerio.GRCz11 with RNAseq aligner STAR The aligned reads were traced back to individual cells and the gene expression level of individual genes were quantified based on the number of UMIs unique molecular indices detected in each cell.The filtered feature cell barcode matrices generated by CellRanger were used for further analysis. Genome build: GRCz11 3.1.0 Supplementary files format and content: Tab delimited text file containing count matrix for each gene and cell 5 dpf embryo Zebrafish were injected with red fluorescent protein RFP expressing UPEC. post 24 hours the zebrafish were dissociated and then homogenate was placed on a glass slide and evaluated for RFP expression on Keyence BZII microscope. Allowed embryos to mature for 4 dpf dpf in a 28.5°C incubator in egg water filled petri dishes. Embryos were collected via visualization through dissecting microscope and separated into control and experimental groups each containing about 30 embryos. The embryos were anesthetized with tricaine and immobilized in methylcellulose. A mixture of the bacterial solution described above phenol red and PBS was made.The mixture was loaded into microneedle and about 1nl of the mixture was injected into the pericardial cavity of each embryo in the experimental group. The control group was injected with 1nl of phenol red and PBS. The embryos were then incubated for 24 hours at 28.5°C. The embryos were euthanized with tricaine and ice added to egg water. The embryos were then added to methylcellulose and the heads of the embryos were removed using a straight blade sterile scalpel. The remaining portion of the embryos were collected and washed 2x with cold PBS at 700g for 5 min then dissociated with Liberase TL Sigma containing DNAse I Sigma in DMEM using gentleMACS Miltenyi Biotec in C tubes then cells were incubated at 370C for 10 minutes with continuous monitoring. When cell homogenate started to disappear DMEM containing 10% FBS was added to stop the dissociation reaction. Cells were then filtered on 70µm filter and centrifuged at 1500 rpm for 10 min. Cells were counted on hemocytometer then dead cells were removed using dead cell removal microbead Miltenyi Biotec with MS column. Live cells were then centrifuged and resuspended in DPBS without xxx+ or Mg2+ and processed for single cell RNA sequencing on 10x genomics platform. Library preparation was performed usingChromium™ Next GEM Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1.   tissue preparation:Single cell suspension|tissue:embryo|age:5 days|treatment:UPEC GSM4855812 GSM4855812: UPEC injected 5 dpf embryo cells; Danio rerio; RNA Seq GSM4855812   1 The embryos were euthanized with tricaine and ice added to egg water. The embryos were then added to methylcellulose and the heads of the embryos were removed using a straight blade sterile scalpel. The remaining portion of the embryos were collected and washed 2x with cold PBS at 700g for 5 min then dissociated with Liberase TL Sigma containing DNAse I Sigma in DMEM using gentleMACS Miltenyi Biotec in C tubes then cells were incubated at 370C for 10 minutes with continuous monitoring. When cell homogenate started to disappear DMEM containing 10% FBS was added to stop the dissociation reaction. Cells were then filtered on 70µm filter and centrifuged at 1500 rpm for 10 min. Cells were counted on hemocytometer then dead cells were removed using dead cell removal microbead Miltenyi Biotec with MS column. Live cells were then centrifuged and resuspended in DPBS without xxx+ or Mg2+ and processed for single cell RNA sequencing on 10x genomics platform. Library preparation was performed usingChromium™ Next GEM Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1. GEO Accession:GSM4855812 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP288474   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Upec S4 L002 I1 001.fastq.gz read2PairFiles=Upec S4 L002 R1 001.fastq.gz read3PairFiles=Upec S4 L002 R2 001.fastq.gz Upec_S4_L002_I1_001.fastq.gz Upec_S4_L002_R1_001.fastq.gz Upec_S4_L002_R2_001.fastq.gz fastq fastq fastq 30699748481.0 241730303.0 GSM4855812 r2 0:8 1:28 2:91 A:8297276041;C:7272515125;G:7096736242;T:8032333424;N:887649 8 28 91   8297276041 7272515125 7096736242 8032333424 887649 SRX9353789 SRS7576887 SRA1147613 GEO Pediatric Nephrology, Indiana University School of Medicine 1 0.94592   0.11122   0.79141   0.51239   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   India 2020-10-25 Larval Larval Embryo Imprecise All anatomical structures
61617 61617 SRR12888599 SRX9353788 SRS7576886 SRP288474 PRJNA671679 Using a Zebrafish Model to Identify Cellular Responses to Uropathogenic E. coli Bacteremia GSE160038 Transcriptome Analysis Urinary tract infections UTIs are the second most common infections encountered in the pediatric population second only to respiratory tract infections. UTIs are also a major cause of morbidity and mortality. UTIs can often ascend causing infection in the upper urinary tract or even progress to bacteremia or urosepsis. Urosepsis accounts for 10 30% of septic shock cases and Uropathogenic E.coli UPEC is responsible for almost 75% of cases. Therefore increased understanding of the effects of urosepsis at the cellular and organ specific level will provide the foundation for improvements in clinical care. Overall design: Two zebrafish cohorts were injected with either sterile saline or UPEC and subjected to scRNA seq. Cell clusters were identified and subjected to RNA velocity analysis. Selected clusters relevant to the innate immune system and bactericidal activity underwent canonical pathway analysis. RNA velocity analysis revealed several key changes in the transcriptional state of UPEC infected cells and pathway analysis provided key information regarding changes in innate immune pathways within the cell clusters.       Saline injected 5 dpf embryo cells GSM4855811   source name:5 dpf embryo|tissue preparation:Single cell suspension|tissue:embryo|age:5 days|treatment:Saline Saline injected 5 dpf embryo cells CellRanger version 3.1 was utilized to process the raw sequence data generated by the sequencer. CellRanger uses bcl2fastq to demultiplex raw base sequence calls generated from the sequencer into sample specific FASTQ files The FASTQ files were then aligned to the zebrafish reference genome Danio rerio.GRCz11 with RNAseq aligner STAR The aligned reads were traced back to individual cells and the gene expression level of individual genes were quantified based on the number of UMIs unique molecular indices detected in each cell.The filtered feature cell barcode matrices generated by CellRanger were used for further analysis. Genome build: GRCz11 3.1.0 Supplementary files format and content: Tab delimited text file containing count matrix for each gene and cell 5 dpf embryo Zebrafish were injected with red fluorescent protein RFP expressing UPEC. post 24 hours the zebrafish were dissociated and then homogenate was placed on a glass slide and evaluated for RFP expression on Keyence BZII microscope. Allowed embryos to mature for 4 dpf dpf in a 28.5°C incubator in egg water filled petri dishes. Embryos were collected via visualization through dissecting microscope and separated into control and experimental groups each containing about 30 embryos. The embryos were anesthetized with tricaine and immobilized in methylcellulose. A mixture of the bacterial solution described above phenol red and PBS was made.The mixture was loaded into microneedle and about 1nl of the mixture was injected into the pericardial cavity of each embryo in the experimental group. The control group was injected with 1nl of phenol red and PBS. The embryos were then incubated for 24 hours at 28.5°C. The embryos were euthanized with tricaine and ice added to egg water. The embryos were then added to methylcellulose and the heads of the embryos were removed using a straight blade sterile scalpel. The remaining portion of the embryos were collected and washed 2x with cold PBS at 700g for 5 min then dissociated with Liberase TL Sigma containing DNAse I Sigma in DMEM using gentleMACS Miltenyi Biotec in C tubes then cells were incubated at 370C for 10 minutes with continuous monitoring. When cell homogenate started to disappear DMEM containing 10% FBS was added to stop the dissociation reaction. Cells were then filtered on 70µm filter and centrifuged at 1500 rpm for 10 min. Cells were counted on hemocytometer then dead cells were removed using dead cell removal microbead Miltenyi Biotec with MS column. Live cells were then centrifuged and resuspended in DPBS without xxx+ or Mg2+ and processed for single cell RNA sequencing on 10x genomics platform. Library preparation was performed usingChromium™ Next GEM Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1.   tissue preparation:Single cell suspension|tissue:embryo|age:5 days|treatment:Saline GSM4855811 GSM4855811: Saline injected 5 dpf embryo cells; Danio rerio; RNA Seq GSM4855811   1 The embryos were euthanized with tricaine and ice added to egg water. The embryos were then added to methylcellulose and the heads of the embryos were removed using a straight blade sterile scalpel. The remaining portion of the embryos were collected and washed 2x with cold PBS at 700g for 5 min then dissociated with Liberase TL Sigma containing DNAse I Sigma in DMEM using gentleMACS Miltenyi Biotec in C tubes then cells were incubated at 370C for 10 minutes with continuous monitoring. When cell homogenate started to disappear DMEM containing 10% FBS was added to stop the dissociation reaction. Cells were then filtered on 70µm filter and centrifuged at 1500 rpm for 10 min. Cells were counted on hemocytometer then dead cells were removed using dead cell removal microbead Miltenyi Biotec with MS column. Live cells were then centrifuged and resuspended in DPBS without xxx+ or Mg2+ and processed for single cell RNA sequencing on 10x genomics platform. Library preparation was performed usingChromium™ Next GEM Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1. GEO Accession:GSM4855811 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP288474   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Saline S3 L001 I1 001.fastq.gz read2PairFiles=Saline S3 L001 R1 001.fastq.gz read3PairFiles=Saline S3 L001 R2 001.fastq.gz Saline_S3_L001_I1_001.fastq.gz Saline_S3_L001_R1_001.fastq.gz Saline_S3_L001_R2_001.fastq.gz fastq fastq fastq 35322876649.0 278132887.0 GSM4855811 r1 0:8 1:28 2:91 A:9928433363;C:8021179562;G:8210286510;T:9162083865;N:893349 8 28 91   9928433363 8021179562 8210286510 9162083865 893349 SRX9353788 SRS7576886 SRA1147613 GEO Pediatric Nephrology, Indiana University School of Medicine 1 0.93984   0.12389   0.81724   0.46893   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   India 2020-10-25 Larval Larval Embryo Imprecise All anatomical structures
61618 61618 SRR12888600 SRX9353788 SRS7576886 SRP288474 PRJNA671679 Using a Zebrafish Model to Identify Cellular Responses to Uropathogenic E. coli Bacteremia GSE160038 Transcriptome Analysis Urinary tract infections UTIs are the second most common infections encountered in the pediatric population second only to respiratory tract infections. UTIs are also a major cause of morbidity and mortality. UTIs can often ascend causing infection in the upper urinary tract or even progress to bacteremia or urosepsis. Urosepsis accounts for 10 30% of septic shock cases and Uropathogenic E.coli UPEC is responsible for almost 75% of cases. Therefore increased understanding of the effects of urosepsis at the cellular and organ specific level will provide the foundation for improvements in clinical care. Overall design: Two zebrafish cohorts were injected with either sterile saline or UPEC and subjected to scRNA seq. Cell clusters were identified and subjected to RNA velocity analysis. Selected clusters relevant to the innate immune system and bactericidal activity underwent canonical pathway analysis. RNA velocity analysis revealed several key changes in the transcriptional state of UPEC infected cells and pathway analysis provided key information regarding changes in innate immune pathways within the cell clusters.       Saline injected 5 dpf embryo cells GSM4855811   source name:5 dpf embryo|tissue preparation:Single cell suspension|tissue:embryo|age:5 days|treatment:Saline Saline injected 5 dpf embryo cells CellRanger version 3.1 was utilized to process the raw sequence data generated by the sequencer. CellRanger uses bcl2fastq to demultiplex raw base sequence calls generated from the sequencer into sample specific FASTQ files The FASTQ files were then aligned to the zebrafish reference genome Danio rerio.GRCz11 with RNAseq aligner STAR The aligned reads were traced back to individual cells and the gene expression level of individual genes were quantified based on the number of UMIs unique molecular indices detected in each cell.The filtered feature cell barcode matrices generated by CellRanger were used for further analysis. Genome build: GRCz11 3.1.0 Supplementary files format and content: Tab delimited text file containing count matrix for each gene and cell 5 dpf embryo Zebrafish were injected with red fluorescent protein RFP expressing UPEC. post 24 hours the zebrafish were dissociated and then homogenate was placed on a glass slide and evaluated for RFP expression on Keyence BZII microscope. Allowed embryos to mature for 4 dpf dpf in a 28.5°C incubator in egg water filled petri dishes. Embryos were collected via visualization through dissecting microscope and separated into control and experimental groups each containing about 30 embryos. The embryos were anesthetized with tricaine and immobilized in methylcellulose. A mixture of the bacterial solution described above phenol red and PBS was made.The mixture was loaded into microneedle and about 1nl of the mixture was injected into the pericardial cavity of each embryo in the experimental group. The control group was injected with 1nl of phenol red and PBS. The embryos were then incubated for 24 hours at 28.5°C. The embryos were euthanized with tricaine and ice added to egg water. The embryos were then added to methylcellulose and the heads of the embryos were removed using a straight blade sterile scalpel. The remaining portion of the embryos were collected and washed 2x with cold PBS at 700g for 5 min then dissociated with Liberase TL Sigma containing DNAse I Sigma in DMEM using gentleMACS Miltenyi Biotec in C tubes then cells were incubated at 370C for 10 minutes with continuous monitoring. When cell homogenate started to disappear DMEM containing 10% FBS was added to stop the dissociation reaction. Cells were then filtered on 70µm filter and centrifuged at 1500 rpm for 10 min. Cells were counted on hemocytometer then dead cells were removed using dead cell removal microbead Miltenyi Biotec with MS column. Live cells were then centrifuged and resuspended in DPBS without xxx+ or Mg2+ and processed for single cell RNA sequencing on 10x genomics platform. Library preparation was performed usingChromium™ Next GEM Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1.   tissue preparation:Single cell suspension|tissue:embryo|age:5 days|treatment:Saline GSM4855811 GSM4855811: Saline injected 5 dpf embryo cells; Danio rerio; RNA Seq GSM4855811   1 The embryos were euthanized with tricaine and ice added to egg water. The embryos were then added to methylcellulose and the heads of the embryos were removed using a straight blade sterile scalpel. The remaining portion of the embryos were collected and washed 2x with cold PBS at 700g for 5 min then dissociated with Liberase TL Sigma containing DNAse I Sigma in DMEM using gentleMACS Miltenyi Biotec in C tubes then cells were incubated at 370C for 10 minutes with continuous monitoring. When cell homogenate started to disappear DMEM containing 10% FBS was added to stop the dissociation reaction. Cells were then filtered on 70µm filter and centrifuged at 1500 rpm for 10 min. Cells were counted on hemocytometer then dead cells were removed using dead cell removal microbead Miltenyi Biotec with MS column. Live cells were then centrifuged and resuspended in DPBS without xxx+ or Mg2+ and processed for single cell RNA sequencing on 10x genomics platform. Library preparation was performed usingChromium™ Next GEM Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1. GEO Accession:GSM4855811 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP288474   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Saline S3 L002 I1 001.fastq.gz read2PairFiles=Saline S3 L002 R1 001.fastq.gz read3PairFiles=Saline S3 L002 R2 001.fastq.gz Saline_S3_L002_I1_001.fastq.gz Saline_S3_L002_R1_001.fastq.gz Saline_S3_L002_R2_001.fastq.gz fastq fastq fastq 35322228695.0 278127785.0 GSM4855811 r2 0:8 1:28 2:91 A:9930368061;C:8021036700;G:8212298286;T:9157497631;N:1028017 8 28 91   9930368061 8021036700 8212298286 9157497631 1028017 SRX9353788 SRS7576886 SRA1147613 GEO Pediatric Nephrology, Indiana University School of Medicine 1 0.93844   0.1252   0.8185   0.47714   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   India 2020-10-25 Larval Larval Embryo Imprecise All anatomical structures
62678 62678 SRR13302564 SRX9731496 SRS7924278 SRP299270 PRJNA687691 The alx3 gene functions to regulate skeletal cell differentiation timing during zebrafish neurocranium development. GSE163826 Other During craniofacial development different populations of cartilage and bone forming cells develop in precise locations in the head. Most of these cells are derived from pluripotent cranial neural crest cells. The mechanisms that divide neural crest cells into distinct populations are not fully understood. Here we use single cell RNA sequencing to transcriptomically define different populations of cranial neural crest cells. We discovered that the transcription factor encoding alx gene family is restricted to the frontonasal population of neural crest cells. Furthermore genetic mutant analyses indicate that alx3 functions to subdivide the frontonasal population into medial versus lateral subpopulations. Our results support a mechanism in which the alx gene family functions as an identity code subdividing frontonasal neural crest cells into distinct subpopulations. This study furthers our understanding of how different skeletal cell fates are established during craniofacial development and how these mechanisms can go awry in genetic diseases. Overall design: neural crest cell profiling of 24 hpf WT D. rerio   pubmed:33741714;pubmed:36134886   WT rep 1 GSM4988014   tissue:Nerual crest cells|tissue source:neuroectoderm|strain:AB strain|age:24 hpf WT rep 1 make ref / make fastq files / aggr command / count command; CellRanger 2.2.0 merge WT and mut data; Seurat v2; e10x < MergeSeuratobject1 = wt object2 = mut project = "n10x" min.cells = 5 min.genes = 100 filter for <250 genes per cell and for any mitochondrial UMIs at less than or equal to 2.5% per cell; Seurat v2; e10x < FilterCellsobject = e10x subset.names = c"nGene" "percent.mito" low.thresholds = c250 Inf high.thresholds = cInf 0.025 cluster projection/dim red. Via PCA/UMAP post WT subset; Seurat v2; nichols TSNE < RunTSNEnichols dr seurat WT dims.use = 1:10 do.fast= TRUE seed.use = 123/nichols umap clusters < FindClustersobject = nichols TSNE reduction.type = "pca" dims.use = 1:15 resolution = 0.2 save.SNN = TRUE n.start = 10 nn.eps = 0.5 print.output = FALSE force.recalc = TRUE/nichols umap clusters < FindClustersobject = nichols TSNE reduction.type = "pca" dims.use = 1:15 resolution = 0.2 save.SNN = TRUE n.start = 10 nn.eps = 0.5 print.output = FALSE force.recalc = TRUE main dim reduction plot; Seurat v2; DimPlotobject = nichols umap clusters reduction.use = "umap" do.return = TRUE pt.size = 1.3 differential expression marker gene ID/localization of expression; Seurat v2; nichols umap.markers1 < FindAllMarkersnichols umap clusters only.pos = TRUE min.pct = 0.1 thresh.use = 0.25/FeaturePlot organizing genes by descending ascending pct.2; Seurat v2; subset based on ascending pct.2 visualize distribution of alx genes across each cluster; Seurat v2; VlnPlotnichols umap clusters features.plot = <each alx gene> single.legend = TRUE y.max = 2 + ggplot2::theme classic + ylab"Expression Level log TPM" pseudotemporal and lineage tracing analyses; mnonocle3 v3; Follows from pseudotime and lineage trajectory mapping vignette for Monocle 3 Trapnell et al. 2014 seurat /featureplot app; Seurat v2 RShiny; FeaturePlotnichols umap clusters diet features = input$gene name reduction = "umap" cols = c"grey" "blue" label = TRUE label.size = 4.5 pt.size = 1.5 ncol = 3 + xlim 1… Nerual crest cells Crispr/cas9 mutagenesis of alx3 gene Jao et al. 2013 Barske et al. 2016 32 double transgenic flia:EGFP;sox10:mRFP embryos were dissociated into single cell suspension using cold active protease from Bacillus licheniformis DNase EDTA and trituration Adam et al. 2017 10X Genomics libraries Animals were maintained and staged according to established protocols Westerfield 1993 Kimmel et al. 1995. tissue source:neuroectoderm|strain:AB strain|age:24 hpf GSM4988014 GSM4988014: WT rep 1; Danio rerio; RNA Seq GSM4988014   1 32 double transgenic flia:EGFP;sox10:mRFP embryos were dissociated into single cell suspension using cold active protease from Bacillus licheniformis DNase EDTA and trituration Adam et al. 2017 10X Genomics libraries GEO Accession:GSM4988014 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP299270     2_mef_wt_High_24hpf_R1_001.fastq.gz 2_mef_wt_High_24hpf_R2_001.fastq.gz fastq fastq 233119629204.0 771919302.0 GSM4988014 r1 0:151 1:151 A:69457580771;C:37624255978;G:33980317215;T:87522302829;N:4535172411 151 151     69457580771 37624255978 33980317215 87522302829 4535172411 SRX9731496 SRS7924278 SRA1177732 GEO Nichols Lab, Craniofacial Biology, University of Colorado - Anschutz Medical Campus 2 0.05174 0.87764 0.00382 0.06802 0.98435 0.84443 0.4489 0.49905 151 151 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-12-24 Pharyngula Embryo Embryo Imprecise All anatomical structures
62848 62848 SRR13402902 SRX9821929 SRS8004722 SRP301260 PRJNA691237 Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways GSE164574 Other The goal of this scRNA seq study was to characterize the pseudo spatial distribution of Nodal and BMP effectors SMADs expression prior to the onset of gastrulation Overall design: scRNA seq was performed on Zebrafish embryos at sphere stage   pubmed:34737283   Zsphere scRNA GSM5014336   tissue:Zebrafish embryos|Stage:sphere Zsphere scRNA We used cell ranger version 2.1.1 to deconvolve align and quantify the per cell transcriptomes. Reads were aligned to version GRCz10 of the zebrafish genome with annotation release 89 from Ensembl software available from 10x genomics. From these alignments we were able to identify 2 644 high quality cells with a mean reads per cell value of 59 754 and a median genes per cell count of 3 807.  All other QC metrics were within thresholds set by 10x Genomics Genome build: GRCz10 release 89 from Ensembl Supplementary files format and content: tar file containing 10x counts matrix features and barcode data Zebrafish embryos   At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle’s Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime Zebrafish embryos were grown in embryo media for dissection of the blastula cup embryos were transferred in DMEM F12 media Stage:sphere GSM5014336 GSM5014336: Zsphere scRNA; Danio rerio; RNA Seq GSM5014336   1 At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle's Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime GEO Accession:GSM5014336 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP301260   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=GUG739A4 S2 L001 I1 001.fastq.gz read2PairFiles=GUG739A4 S2 L001 R1 001.fastq.gz read3PairFiles=GUG739A4 S2 L001 R2 001.fastq.gz GUG739A4_S2_L001_I1_001.fastq.gz GUG739A4_S2_L001_R1_001.fastq.gz GUG739A4_S2_L001_R2_001.fastq.gz fastq fastq fastq 5235400170.0 24930477.0 GSM5014336 r1 0:8 1:101 2:101 A:1177347684;C:925887308;G:939712357;T:2191666659;N:786162 8 101 101   1177347684 925887308 939712357 2191666659 786162 SRX9821929 SRS8004722 SRA1182478 GEO Bioinformatics, Bioinformatics, The Francis Crick Institute 1 0.91081   0.11647   0.78459   0.5629   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2021-01-11 Blastula Embryo Embryo Imprecise All anatomical structures
62849 62849 SRR13402903 SRX9821929 SRS8004722 SRP301260 PRJNA691237 Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways GSE164574 Other The goal of this scRNA seq study was to characterize the pseudo spatial distribution of Nodal and BMP effectors SMADs expression prior to the onset of gastrulation Overall design: scRNA seq was performed on Zebrafish embryos at sphere stage   pubmed:34737283   Zsphere scRNA GSM5014336   tissue:Zebrafish embryos|Stage:sphere Zsphere scRNA We used cell ranger version 2.1.1 to deconvolve align and quantify the per cell transcriptomes. Reads were aligned to version GRCz10 of the zebrafish genome with annotation release 89 from Ensembl software available from 10x genomics. From these alignments we were able to identify 2 644 high quality cells with a mean reads per cell value of 59 754 and a median genes per cell count of 3 807.  All other QC metrics were within thresholds set by 10x Genomics Genome build: GRCz10 release 89 from Ensembl Supplementary files format and content: tar file containing 10x counts matrix features and barcode data Zebrafish embryos   At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle’s Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime Zebrafish embryos were grown in embryo media for dissection of the blastula cup embryos were transferred in DMEM F12 media Stage:sphere GSM5014336 GSM5014336: Zsphere scRNA; Danio rerio; RNA Seq GSM5014336   1 At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle's Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime GEO Accession:GSM5014336 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP301260   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=GUG739A4 S2 L002 I1 001.fastq.gz read2PairFiles=GUG739A4 S2 L002 R1 001.fastq.gz read3PairFiles=GUG739A4 S2 L002 R2 001.fastq.gz GUG739A4_S2_L002_I1_001.fastq.gz GUG739A4_S2_L002_R1_001.fastq.gz GUG739A4_S2_L002_R2_001.fastq.gz fastq fastq fastq 5543517210.0 26397701.0 GSM5014336 r2 0:8 1:101 2:101 A:1240643673;C:980694158;G:992958309;T:2328732820;N:488250 8 101 101   1240643673 980694158 992958309 2328732820 488250 SRX9821929 SRS8004722 SRA1182478 GEO Bioinformatics, Bioinformatics, The Francis Crick Institute 1 0.91665   0.11529   0.78472   0.58007   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2021-01-11 Blastula Embryo Embryo Imprecise All anatomical structures
62850 62850 SRR13402904 SRX9821929 SRS8004722 SRP301260 PRJNA691237 Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways GSE164574 Other The goal of this scRNA seq study was to characterize the pseudo spatial distribution of Nodal and BMP effectors SMADs expression prior to the onset of gastrulation Overall design: scRNA seq was performed on Zebrafish embryos at sphere stage   pubmed:34737283   Zsphere scRNA GSM5014336   tissue:Zebrafish embryos|Stage:sphere Zsphere scRNA We used cell ranger version 2.1.1 to deconvolve align and quantify the per cell transcriptomes. Reads were aligned to version GRCz10 of the zebrafish genome with annotation release 89 from Ensembl software available from 10x genomics. From these alignments we were able to identify 2 644 high quality cells with a mean reads per cell value of 59 754 and a median genes per cell count of 3 807.  All other QC metrics were within thresholds set by 10x Genomics Genome build: GRCz10 release 89 from Ensembl Supplementary files format and content: tar file containing 10x counts matrix features and barcode data Zebrafish embryos   At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle’s Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime Zebrafish embryos were grown in embryo media for dissection of the blastula cup embryos were transferred in DMEM F12 media Stage:sphere GSM5014336 GSM5014336: Zsphere scRNA; Danio rerio; RNA Seq GSM5014336   1 At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle's Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime GEO Accession:GSM5014336 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP301260   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=GUG739A4 S2 L003 I1 001.fastq.gz read2PairFiles=GUG739A4 S2 L003 R1 001.fastq.gz read3PairFiles=GUG739A4 S2 L003 R2 001.fastq.gz GUG739A4_S2_L003_I1_001.fastq.gz GUG739A4_S2_L003_R1_001.fastq.gz GUG739A4_S2_L003_R2_001.fastq.gz fastq fastq fastq 5572550130.0 26535953.0 GSM5014336 r3 0:8 1:101 2:101 A:1249457035;C:994601699;G:1005584984;T:2322470542;N:435870 8 101 101   1249457035 994601699 1005584984 2322470542 435870 SRX9821929 SRS8004722 SRA1182478 GEO Bioinformatics, Bioinformatics, The Francis Crick Institute 1 0.90814   0.11693   0.78565   0.57928   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2021-01-11 Blastula Embryo Embryo Imprecise All anatomical structures
62851 62851 SRR13402905 SRX9821929 SRS8004722 SRP301260 PRJNA691237 Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways GSE164574 Other The goal of this scRNA seq study was to characterize the pseudo spatial distribution of Nodal and BMP effectors SMADs expression prior to the onset of gastrulation Overall design: scRNA seq was performed on Zebrafish embryos at sphere stage   pubmed:34737283   Zsphere scRNA GSM5014336   tissue:Zebrafish embryos|Stage:sphere Zsphere scRNA We used cell ranger version 2.1.1 to deconvolve align and quantify the per cell transcriptomes. Reads were aligned to version GRCz10 of the zebrafish genome with annotation release 89 from Ensembl software available from 10x genomics. From these alignments we were able to identify 2 644 high quality cells with a mean reads per cell value of 59 754 and a median genes per cell count of 3 807.  All other QC metrics were within thresholds set by 10x Genomics Genome build: GRCz10 release 89 from Ensembl Supplementary files format and content: tar file containing 10x counts matrix features and barcode data Zebrafish embryos   At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle’s Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime Zebrafish embryos were grown in embryo media for dissection of the blastula cup embryos were transferred in DMEM F12 media Stage:sphere GSM5014336 GSM5014336: Zsphere scRNA; Danio rerio; RNA Seq GSM5014336   1 At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle's Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime GEO Accession:GSM5014336 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP301260   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=GUG739A4 S2 L004 I1 001.fastq.gz read2PairFiles=GUG739A4 S2 L004 R1 001.fastq.gz read3PairFiles=GUG739A4 S2 L004 R2 001.fastq.gz GUG739A4_S2_L004_I1_001.fastq.gz GUG739A4_S2_L004_R1_001.fastq.gz GUG739A4_S2_L004_R2_001.fastq.gz fastq fastq fastq 5614329210.0 26734901.0 GSM5014336 r4 0:8 1:101 2:101 A:1257192667;C:993041786;G:1007516062;T:2349738132;N:6840563 8 101 101   1257192667 993041786 1007516062 2349738132 6840563 SRX9821929 SRS8004722 SRA1182478 GEO Bioinformatics, Bioinformatics, The Francis Crick Institute 1 0.91345   0.11553   0.78632   0.58232   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2021-01-11 Blastula Embryo Embryo Imprecise All anatomical structures
62852 62852 SRR13402906 SRX9821929 SRS8004722 SRP301260 PRJNA691237 Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways GSE164574 Other The goal of this scRNA seq study was to characterize the pseudo spatial distribution of Nodal and BMP effectors SMADs expression prior to the onset of gastrulation Overall design: scRNA seq was performed on Zebrafish embryos at sphere stage   pubmed:34737283   Zsphere scRNA GSM5014336   tissue:Zebrafish embryos|Stage:sphere Zsphere scRNA We used cell ranger version 2.1.1 to deconvolve align and quantify the per cell transcriptomes. Reads were aligned to version GRCz10 of the zebrafish genome with annotation release 89 from Ensembl software available from 10x genomics. From these alignments we were able to identify 2 644 high quality cells with a mean reads per cell value of 59 754 and a median genes per cell count of 3 807.  All other QC metrics were within thresholds set by 10x Genomics Genome build: GRCz10 release 89 from Ensembl Supplementary files format and content: tar file containing 10x counts matrix features and barcode data Zebrafish embryos   At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle’s Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime Zebrafish embryos were grown in embryo media for dissection of the blastula cup embryos were transferred in DMEM F12 media Stage:sphere GSM5014336 GSM5014336: Zsphere scRNA; Danio rerio; RNA Seq GSM5014336   1 At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle's Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime GEO Accession:GSM5014336 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP301260   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=GUG739A4 S2 L005 I1 001.fastq.gz read2PairFiles=GUG739A4 S2 L005 R1 001.fastq.gz read3PairFiles=GUG739A4 S2 L005 R2 001.fastq.gz GUG739A4_S2_L005_I1_001.fastq.gz GUG739A4_S2_L005_R1_001.fastq.gz GUG739A4_S2_L005_R2_001.fastq.gz fastq fastq fastq 5660581290.0 26955149.0 GSM5014336 r5 0:8 1:101 2:101 A:1268509148;C:1023948185;G:1033027319;T:2334888489;N:208149 8 101 101   1268509148 1023948185 1033027319 2334888489 208149 SRX9821929 SRS8004722 SRA1182478 GEO Bioinformatics, Bioinformatics, The Francis Crick Institute 1 0.91009   0.11843   0.78599   0.57826   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2021-01-11 Blastula Embryo Embryo Imprecise All anatomical structures
62853 62853 SRR13402907 SRX9821929 SRS8004722 SRP301260 PRJNA691237 Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways GSE164574 Other The goal of this scRNA seq study was to characterize the pseudo spatial distribution of Nodal and BMP effectors SMADs expression prior to the onset of gastrulation Overall design: scRNA seq was performed on Zebrafish embryos at sphere stage   pubmed:34737283   Zsphere scRNA GSM5014336   tissue:Zebrafish embryos|Stage:sphere Zsphere scRNA We used cell ranger version 2.1.1 to deconvolve align and quantify the per cell transcriptomes. Reads were aligned to version GRCz10 of the zebrafish genome with annotation release 89 from Ensembl software available from 10x genomics. From these alignments we were able to identify 2 644 high quality cells with a mean reads per cell value of 59 754 and a median genes per cell count of 3 807.  All other QC metrics were within thresholds set by 10x Genomics Genome build: GRCz10 release 89 from Ensembl Supplementary files format and content: tar file containing 10x counts matrix features and barcode data Zebrafish embryos   At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle’s Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime Zebrafish embryos were grown in embryo media for dissection of the blastula cup embryos were transferred in DMEM F12 media Stage:sphere GSM5014336 GSM5014336: Zsphere scRNA; Danio rerio; RNA Seq GSM5014336   1 At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle's Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime GEO Accession:GSM5014336 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP301260   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=GUG739A4 S2 L006 I1 001.fastq.gz read2PairFiles=GUG739A4 S2 L006 R1 001.fastq.gz read3PairFiles=GUG739A4 S2 L006 R2 001.fastq.gz GUG739A4_S2_L006_I1_001.fastq.gz GUG739A4_S2_L006_R1_001.fastq.gz GUG739A4_S2_L006_R2_001.fastq.gz fastq fastq fastq 5551742700.0 26436870.0 GSM5014336 r6 0:8 1:101 2:101 A:1244015771;C:994654836;G:1005415645;T:2307255998;N:400450 8 101 101   1244015771 994654836 1005415645 2307255998 400450 SRX9821929 SRS8004722 SRA1182478 GEO Bioinformatics, Bioinformatics, The Francis Crick Institute 1 0.90906   0.11635   0.78421   0.5674   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2021-01-11 Blastula Embryo Embryo Imprecise All anatomical structures
63038 63038 SRR13565188 SRX9963432 SRS8137098 SRP303506 PRJNA695274 Single cell response landscape of graded Nodal signaling in zebrafish explants [single cell RNA seq] GSE165653 Transcriptome Analysis Purpose: To construct cell landscape of graded Nodal signaling in zebrafish explants. Methods: Nodal injected explants injected with 10pg ndr2 mRNA were harvested at xxxhpf 5hpf 6hpf 8hpf 10hpf 24hpf. Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 42 317 single cell transcriptomes were collected post stringent quality control measures. Conclusions: 19 Cell types from 6 developmental stages were identified Nodal explant mainly contains the axial mesoderm prechordal plate and notochord and anterior posterior patterned head structures. Overall design: zebrafish explants injected with 10pg ndr2 mRNA were harvested at xxxhpf 5hpf 6hpf 8hpf 10hpf 24hpf for scRNA seq. parent bioproject:PRJNA695267 pubmed:37729057   zebrafish Nodal explants 24hpf GSM5047616   source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:24hpf|treatment:injected with 10pg ndr2 mRNA zebrafish Nodal explants 24hpf Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 or GRCz10 using the 10x Genomics CellRanger pipeline version 2.1.1 with default parameters. Genome build: GRCz11/GRCz10 Supplementary files format and content: tar compressed files included filtered gene bc matrices post running CellRanger pipeline zebrafish cells 10pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf 8hpf 10hpf and 24hpf corresponding to embryonic developmental stage separately. Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer’s protocol for 10000 cells recovery. explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium strain:AB|tissue:embryonic cells|age:24hpf|treatment:injected with 10pg ndr2 mRNA GSM5047616 GSM5047616: zebrafish Nodal explants 24hpf; Danio rerio; RNA Seq GSM5047616   1 Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer's protocol for 10000 cells recovery. GEO Accession:GSM5047616 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP303506     wt_cyc_24hpf_S2_L001_R1_001.fastq.gz wt_cyc_24hpf_S2_L001_R2_001.fastq.gz fastq fastq 90396710760.0 510715880.0 GSM5047616 r1 0:26 1:151 A:26454729080;C:19389596055;G:21032365903;T:23518029586;N:1990136 26 151     26454729080 19389596055 21032365903 23518029586 1990136 SRX9963432 SRS8137098 SRA1188621 GEO Institute of genetics, Zhejiang University 2 0.00326 0.92286 0.00081 0.07546 0.99265 0.81288 0.43855 0.51651 26 151 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2021-01-27 Pharyngula Embryo Embryo Imprecise All anatomical structures
63039 63039 SRR13565187 SRX9963431 SRS8137097 SRP303506 PRJNA695274 Single cell response landscape of graded Nodal signaling in zebrafish explants [single cell RNA seq] GSE165653 Transcriptome Analysis Purpose: To construct cell landscape of graded Nodal signaling in zebrafish explants. Methods: Nodal injected explants injected with 10pg ndr2 mRNA were harvested at xxxhpf 5hpf 6hpf 8hpf 10hpf 24hpf. Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 42 317 single cell transcriptomes were collected post stringent quality control measures. Conclusions: 19 Cell types from 6 developmental stages were identified Nodal explant mainly contains the axial mesoderm prechordal plate and notochord and anterior posterior patterned head structures. Overall design: zebrafish explants injected with 10pg ndr2 mRNA were harvested at xxxhpf 5hpf 6hpf 8hpf 10hpf 24hpf for scRNA seq. parent bioproject:PRJNA695267 pubmed:37729057   zebrafish Nodal explants 10hpf GSM5047615   source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:10hpf|treatment:injected with 10pg ndr2 mRNA zebrafish Nodal explants 10hpf Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 or GRCz10 using the 10x Genomics CellRanger pipeline version 2.1.1 with default parameters. Genome build: GRCz11/GRCz10 Supplementary files format and content: tar compressed files included filtered gene bc matrices post running CellRanger pipeline zebrafish cells 10pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf 8hpf 10hpf and 24hpf corresponding to embryonic developmental stage separately. Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer’s protocol for 10000 cells recovery. explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium strain:AB|tissue:embryonic cells|age:10hpf|treatment:injected with 10pg ndr2 mRNA GSM5047615 GSM5047615: zebrafish Nodal explants 10hpf; Danio rerio; RNA Seq GSM5047615   1 Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer's protocol for 10000 cells recovery. GEO Accession:GSM5047615 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP303506     wt_cyc_10hpf_S4_L002_R1_001.fastq.gz wt_cyc_10hpf_S4_L002_R2_001.fastq.gz fastq fastq 91961453064.0 519556232.0 GSM5047615 r1 0:26 1:151 A:27264345194;C:18865491810;G:20605255683;T:25224284164;N:2076213 26 151     27264345194 18865491810 20605255683 25224284164 2076213 SRX9963431 SRS8137097 SRA1188621 GEO Institute of genetics, Zhejiang University 2 0.00462 0.90539 0.00122 0.10015 0.99022 0.81513 0.43095 0.51015 26 151 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2021-01-27 Gastrula Embryo Embryo Imprecise All anatomical structures
63040 63040 SRR13565186 SRX9963430 SRS8137096 SRP303506 PRJNA695274 Single cell response landscape of graded Nodal signaling in zebrafish explants [single cell RNA seq] GSE165653 Transcriptome Analysis Purpose: To construct cell landscape of graded Nodal signaling in zebrafish explants. Methods: Nodal injected explants injected with 10pg ndr2 mRNA were harvested at xxxhpf 5hpf 6hpf 8hpf 10hpf 24hpf. Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 42 317 single cell transcriptomes were collected post stringent quality control measures. Conclusions: 19 Cell types from 6 developmental stages were identified Nodal explant mainly contains the axial mesoderm prechordal plate and notochord and anterior posterior patterned head structures. Overall design: zebrafish explants injected with 10pg ndr2 mRNA were harvested at xxxhpf 5hpf 6hpf 8hpf 10hpf 24hpf for scRNA seq. parent bioproject:PRJNA695267 pubmed:37729057   zebrafish Nodal explants 8hpf GSM5047614   source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:8hpf|treatment:injected with 10pg ndr2 mRNA zebrafish Nodal explants 8hpf Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 or GRCz10 using the 10x Genomics CellRanger pipeline version 2.1.1 with default parameters. Genome build: GRCz11/GRCz10 Supplementary files format and content: tar compressed files included filtered gene bc matrices post running CellRanger pipeline zebrafish cells 10pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf 8hpf 10hpf and 24hpf corresponding to embryonic developmental stage separately. Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer’s protocol for 10000 cells recovery. explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium strain:AB|tissue:embryonic cells|age:8hpf|treatment:injected with 10pg ndr2 mRNA GSM5047614 GSM5047614: zebrafish Nodal explants 8hpf; Danio rerio; RNA Seq GSM5047614   1 Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer's protocol for 10000 cells recovery. GEO Accession:GSM5047614 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP303506     wt_cyc_8hpf_S3_L002_R1_001.fastq.gz wt_cyc_8hpf_S3_L002_R2_001.fastq.gz fastq fastq 85243156635.0 481599755.0 GSM5047614 r1 0:26 1:151 A:25256590409;C:17389002254;G:18983505108;T:23612132946;N:1925918 26 151     25256590409 17389002254 18983505108 23612132946 1925918 SRX9963430 SRS8137096 SRA1188621 GEO Institute of genetics, Zhejiang University 2 0.00722 0.90801 0.0016 0.10314 0.98545 0.80931 0.45087 0.53205 26 151 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2021-01-27 Gastrula Embryo Embryo Imprecise All anatomical structures
63041 63041 SRR13565185 SRX9963429 SRS8137099 SRP303506 PRJNA695274 Single cell response landscape of graded Nodal signaling in zebrafish explants [single cell RNA seq] GSE165653 Transcriptome Analysis Purpose: To construct cell landscape of graded Nodal signaling in zebrafish explants. Methods: Nodal injected explants injected with 10pg ndr2 mRNA were harvested at xxxhpf 5hpf 6hpf 8hpf 10hpf 24hpf. Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 42 317 single cell transcriptomes were collected post stringent quality control measures. Conclusions: 19 Cell types from 6 developmental stages were identified Nodal explant mainly contains the axial mesoderm prechordal plate and notochord and anterior posterior patterned head structures. Overall design: zebrafish explants injected with 10pg ndr2 mRNA were harvested at xxxhpf 5hpf 6hpf 8hpf 10hpf 24hpf for scRNA seq. parent bioproject:PRJNA695267 pubmed:37729057   zebrafish Nodal explants 6hpf GSM5047613   source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 10pg ndr2 mRNA zebrafish Nodal explants 6hpf Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 or GRCz10 using the 10x Genomics CellRanger pipeline version 2.1.1 with default parameters. Genome build: GRCz11/GRCz10 Supplementary files format and content: tar compressed files included filtered gene bc matrices post running CellRanger pipeline zebrafish cells 10pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf 8hpf 10hpf and 24hpf corresponding to embryonic developmental stage separately. Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer’s protocol for 10000 cells recovery. explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 10pg ndr2 mRNA GSM5047613 GSM5047613: zebrafish Nodal explants 6hpf; Danio rerio; RNA Seq GSM5047613   1 Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer's protocol for 10000 cells recovery. GEO Accession:GSM5047613 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP303506     wt_cyc_6hpf_S1_L004_R1_001.fastq.gz wt_cyc_6hpf_S1_L004_R2_001.fastq.gz fastq fastq 120375311594.0 398593747.0 GSM5047613 r1 0:151 1:151 A:31070717775;C:21268441476;G:21658594109;T:46362015215;N:15543019 151 151     31070717775 21268441476 21658594109 46362015215 15543019 SRX9963429 SRS8137099 SRA1188621 GEO Institute of genetics, Zhejiang University 2 0.11581 0.88209 0.0154 0.11076 0.97153 0.79813 0.51657 0.53551 151 151 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2021-01-27 Gastrula Embryo Embryo Imprecise All anatomical structures
63042 63042 SRR13565184 SRX9963428 SRS8137095 SRP303506 PRJNA695274 Single cell response landscape of graded Nodal signaling in zebrafish explants [single cell RNA seq] GSE165653 Transcriptome Analysis Purpose: To construct cell landscape of graded Nodal signaling in zebrafish explants. Methods: Nodal injected explants injected with 10pg ndr2 mRNA were harvested at xxxhpf 5hpf 6hpf 8hpf 10hpf 24hpf. Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 42 317 single cell transcriptomes were collected post stringent quality control measures. Conclusions: 19 Cell types from 6 developmental stages were identified Nodal explant mainly contains the axial mesoderm prechordal plate and notochord and anterior posterior patterned head structures. Overall design: zebrafish explants injected with 10pg ndr2 mRNA were harvested at xxxhpf 5hpf 6hpf 8hpf 10hpf 24hpf for scRNA seq. parent bioproject:PRJNA695267 pubmed:37729057   zebrafish Nodal explants 5hpf GSM5047612   source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:5hpf|treatment:injected with 10pg ndr2 mRNA zebrafish Nodal explants 5hpf Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 or GRCz10 using the 10x Genomics CellRanger pipeline version 2.1.1 with default parameters. Genome build: GRCz11/GRCz10 Supplementary files format and content: tar compressed files included filtered gene bc matrices post running CellRanger pipeline zebrafish cells 10pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf 8hpf 10hpf and 24hpf corresponding to embryonic developmental stage separately. Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer’s protocol for 10000 cells recovery. explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium strain:AB|tissue:embryonic cells|age:5hpf|treatment:injected with 10pg ndr2 mRNA GSM5047612 GSM5047612: zebrafish Nodal explants 5hpf; Danio rerio; RNA Seq GSM5047612   1 Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer's protocol for 10000 cells recovery. GEO Accession:GSM5047612 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP303506     wt_cyc_5hpf_S1_L002_R1_001.fastq.gz wt_cyc_5hpf_S1_L002_R2_001.fastq.gz fastq fastq 132074187896.0 437331748.0 GSM5047612 r1 0:151 1:151 A:33956635680;C:22833737374;G:24573359678;T:50703117357;N:7337807 151 151     33956635680 22833737374 24573359678 50703117357 7337807 SRX9963428 SRS8137095 SRA1188621 GEO Institute of genetics, Zhejiang University 2 0.25456 0.90744 0.02797 0.06895 0.96999 0.79732 0.57673 0.63217 151 151 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2021-01-27 Blastula Embryo Embryo Imprecise All anatomical structures
63043 63043 SRR13565183 SRX9963427 SRS8137094 SRP303506 PRJNA695274 Single cell response landscape of graded Nodal signaling in zebrafish explants [single cell RNA seq] GSE165653 Transcriptome Analysis Purpose: To construct cell landscape of graded Nodal signaling in zebrafish explants. Methods: Nodal injected explants injected with 10pg ndr2 mRNA were harvested at xxxhpf 5hpf 6hpf 8hpf 10hpf 24hpf. Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 42 317 single cell transcriptomes were collected post stringent quality control measures. Conclusions: 19 Cell types from 6 developmental stages were identified Nodal explant mainly contains the axial mesoderm prechordal plate and notochord and anterior posterior patterned head structures. Overall design: zebrafish explants injected with 10pg ndr2 mRNA were harvested at xxxhpf 5hpf 6hpf 8hpf 10hpf 24hpf for scRNA seq. parent bioproject:PRJNA695267 pubmed:37729057   zebrafish Nodal explants 4hpf GSM5047611   source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:4hpf|treatment:injected with 10pg ndr2 mRNA zebrafish Nodal explants 4hpf Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 or GRCz10 using the 10x Genomics CellRanger pipeline version 2.1.1 with default parameters. Genome build: GRCz11/GRCz10 Supplementary files format and content: tar compressed files included filtered gene bc matrices post running CellRanger pipeline zebrafish cells 10pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf 8hpf 10hpf and 24hpf corresponding to embryonic developmental stage separately. Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer’s protocol for 10000 cells recovery. explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium strain:AB|tissue:embryonic cells|age:4hpf|treatment:injected with 10pg ndr2 mRNA GSM5047611 GSM5047611: zebrafish Nodal explants 4hpf; Danio rerio; RNA Seq GSM5047611   1 Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer's protocol for 10000 cells recovery. GEO Accession:GSM5047611 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP303506     wt_cyc_4hpf_S1_L007_R1_001.fastq.gz wt_cyc_4hpf_S1_L007_R2_001.fastq.gz fastq fastq 131011503350.0 433812925.0 GSM5047611 r1 0:151 1:151 A:33733394074;C:20387214801;G:21857805230;T:55019780406;N:13308839 151 151     33733394074 20387214801 21857805230 55019780406 13308839 SRX9963427 SRS8137094 SRA1188621 GEO Institute of genetics, Zhejiang University 2 0.34825 0.89448 0.03615 0.09865 0.94456 0.77555 0.51973 0.48621 151 151 B B mate1-mate2 similar by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2021-01-27 Blastula Embryo Embryo Imprecise All anatomical structures
63459 63459 SRR13839977 SRX10218349 SRS8363298 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 18 hpf second data set GSM5129559   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:18 hpf|cell type:NC cell FACS sorted NC cells 18 hpf second data set FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:18 hpf|cell type:NC cell GSM5129559 GSM5129559: FACS sorted NC cells 18 hpf second data set; Danio rerio; RNA Seq GSM5129559   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129559 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=18hpf Arch1 S29 L002 I1 001.fastq.gz read2PairFiles=18hpf Arch1 S29 L002 R1 001.fastq.gz read3PairFiles=18hpf Arch1 S29 L002 R2 001.fastq.gz 18hpf_Arch1_S29_L002_I1_001.fastq.gz 18hpf_Arch1_S29_L002_R1_001.fastq.gz 18hpf_Arch1_S29_L002_R2_001.fastq.gz fastq fastq fastq 4052921409.0 31912767.0 GSM5129559 r1 0:8 1:28 2:91 A:1136950757;C:991564617;G:926017760;T:998239129;N:149146 8 28 91   1136950757 991564617 926017760 998239129 149146 SRX10218349 SRS8363298 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.93266   0.14931   0.79807   0.54283   91   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures
63460 63460 SRR13839978 SRX10218349 SRS8363298 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 18 hpf second data set GSM5129559   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:18 hpf|cell type:NC cell FACS sorted NC cells 18 hpf second data set FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:18 hpf|cell type:NC cell GSM5129559 GSM5129559: FACS sorted NC cells 18 hpf second data set; Danio rerio; RNA Seq GSM5129559   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129559 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=18hpf Arch1 S30 L002 I1 001.fastq.gz read2PairFiles=18hpf Arch1 S30 L002 R1 001.fastq.gz read3PairFiles=18hpf Arch1 S30 L002 R2 001.fastq.gz 18hpf_Arch1_S30_L002_I1_001.fastq.gz 18hpf_Arch1_S30_L002_R1_001.fastq.gz 18hpf_Arch1_S30_L002_R2_001.fastq.gz fastq fastq fastq 4259203318.0 33537034.0 GSM5129559 r2 0:8 1:28 2:91 A:1127048655;C:943981129;G:1070702144;T:1117317098;N:154292 8 28 91   1127048655 943981129 1070702144 1117317098 154292 SRX10218349 SRS8363298 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.93278   0.15063   0.79401   0.53078   91   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures
63461 63461 SRR13839979 SRX10218349 SRS8363298 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 18 hpf second data set GSM5129559   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:18 hpf|cell type:NC cell FACS sorted NC cells 18 hpf second data set FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:18 hpf|cell type:NC cell GSM5129559 GSM5129559: FACS sorted NC cells 18 hpf second data set; Danio rerio; RNA Seq GSM5129559   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129559 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=18hpf Arch1 S31 L002 I1 001.fastq.gz read2PairFiles=18hpf Arch1 S31 L002 R1 001.fastq.gz read3PairFiles=18hpf Arch1 S31 L002 R2 001.fastq.gz 18hpf_Arch1_S31_L002_I1_001.fastq.gz 18hpf_Arch1_S31_L002_R1_001.fastq.gz 18hpf_Arch1_S31_L002_R2_001.fastq.gz fastq fastq fastq 5413095600.0 42622800.0 GSM5129559 r3 0:8 1:28 2:91 A:1388741729;C:1240757967;G:1364860623;T:1418539451;N:195830 8 28 91   1388741729 1240757967 1364860623 1418539451 195830 SRX10218349 SRS8363298 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.93311   0.15022   0.79413   0.52512   91   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures
63462 63462 SRR13839980 SRX10218349 SRS8363298 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 18 hpf second data set GSM5129559   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:18 hpf|cell type:NC cell FACS sorted NC cells 18 hpf second data set FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:18 hpf|cell type:NC cell GSM5129559 GSM5129559: FACS sorted NC cells 18 hpf second data set; Danio rerio; RNA Seq GSM5129559   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129559 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=18hpf Arch1 S32 L002 I1 001.fastq.gz read2PairFiles=18hpf Arch1 S32 L002 R1 001.fastq.gz read3PairFiles=18hpf Arch1 S32 L002 R2 001.fastq.gz 18hpf_Arch1_S32_L002_I1_001.fastq.gz 18hpf_Arch1_S32_L002_R1_001.fastq.gz 18hpf_Arch1_S32_L002_R2_001.fastq.gz fastq fastq fastq 3654920935.0 28778905.0 GSM5129559 r4 0:8 1:28 2:91 A:1052843448;C:808525754;G:892737353;T:900683233;N:131147 8 28 91   1052843448 808525754 892737353 900683233 131147 SRX10218349 SRS8363298 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.9332   0.15094   0.79539   0.52391   91   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures
63463 63463 SRR13839973 SRX10218348 SRS8363299 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 30 hpf GSM5129558   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:30 hpf|cell type:NC cell FACS sorted NC cells 30 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:30 hpf|cell type:NC cell GSM5129558 GSM5129558: FACS sorted NC cells 30 hpf; Danio rerio; RNA Seq GSM5129558   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129558 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 30hpf sample2 S13 L002 I1 001.fastq.gz read2PairFiles=Arch 1 30hpf sample2 S13 L002 R1 001.fastq.gz read3PairFiles=Arch 1 30hpf sample2 S13 L002 R2 001.fastq.gz Arch_1_30hpf_sample2_S13_L002_I1_001.fastq.gz Arch_1_30hpf_sample2_S13_L002_R1_001.fastq.gz Arch_1_30hpf_sample2_S13_L002_R2_001.fastq.gz fastq fastq fastq 3858413856.0 29230408.0 GSM5129558 r1 0:8 1:26 2:98 A:1102639781;C:884133865;G:864837660;T:1005997593;N:804957 8 26 98   1102639781 884133865 864837660 1005997593 804957 SRX10218348 SRS8363299 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.93149   0.08085   0.83136   0.50094   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
63464 63464 SRR13839974 SRX10218348 SRS8363299 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 30 hpf GSM5129558   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:30 hpf|cell type:NC cell FACS sorted NC cells 30 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:30 hpf|cell type:NC cell GSM5129558 GSM5129558: FACS sorted NC cells 30 hpf; Danio rerio; RNA Seq GSM5129558   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129558 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 30hpf sample2 S14 L002 I1 001.fastq.gz read2PairFiles=Arch 1 30hpf sample2 S14 L002 R1 001.fastq.gz read3PairFiles=Arch 1 30hpf sample2 S14 L002 R2 001.fastq.gz Arch_1_30hpf_sample2_S14_L002_I1_001.fastq.gz Arch_1_30hpf_sample2_S14_L002_R1_001.fastq.gz Arch_1_30hpf_sample2_S14_L002_R2_001.fastq.gz fastq fastq fastq 3665958912.0 27772416.0 GSM5129558 r2 0:8 1:26 2:98 A:968281188;C:811092950;G:819421562;T:1066395868;N:767344 8 26 98   968281188 811092950 819421562 1066395868 767344 SRX10218348 SRS8363299 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.93208   0.08162   0.83222   0.50631   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
63465 63465 SRR13839975 SRX10218348 SRS8363299 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 30 hpf GSM5129558   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:30 hpf|cell type:NC cell FACS sorted NC cells 30 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:30 hpf|cell type:NC cell GSM5129558 GSM5129558: FACS sorted NC cells 30 hpf; Danio rerio; RNA Seq GSM5129558   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129558 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 30hpf sample2 S15 L002 I1 001.fastq.gz read2PairFiles=Arch 1 30hpf sample2 S15 L002 R1 001.fastq.gz read3PairFiles=Arch 1 30hpf sample2 S15 L002 R2 001.fastq.gz Arch_1_30hpf_sample2_S15_L002_I1_001.fastq.gz Arch_1_30hpf_sample2_S15_L002_R1_001.fastq.gz Arch_1_30hpf_sample2_S15_L002_R2_001.fastq.gz fastq fastq fastq 77677116.0 588463.0 GSM5129558 r3 0:8 1:26 2:98 A:23976702;C:16463710;G:17540603;T:19680514;N:15587 8 26 98   23976702 16463710 17540603 19680514 15587 SRX10218348 SRS8363299 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.92692   0.08807   0.86862   0.51197   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
63466 63466 SRR13839976 SRX10218348 SRS8363299 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 30 hpf GSM5129558   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:30 hpf|cell type:NC cell FACS sorted NC cells 30 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:30 hpf|cell type:NC cell GSM5129558 GSM5129558: FACS sorted NC cells 30 hpf; Danio rerio; RNA Seq GSM5129558   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129558 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 30hpf sample2 S16 L002 I1 001.fastq.gz read2PairFiles=Arch 1 30hpf sample2 S16 L002 R1 001.fastq.gz read3PairFiles=Arch 1 30hpf sample2 S16 L002 R2 001.fastq.gz Arch_1_30hpf_sample2_S16_L002_I1_001.fastq.gz Arch_1_30hpf_sample2_S16_L002_R1_001.fastq.gz Arch_1_30hpf_sample2_S16_L002_R2_001.fastq.gz fastq fastq fastq 2780455656.0 21064058.0 GSM5129558 r4 0:8 1:26 2:98 A:820298309;C:594384917;G:661749022;T:703442989;N:580419 8 26 98   820298309 594384917 661749022 703442989 580419 SRX10218348 SRS8363299 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.93161   0.0813   0.83741   0.49845   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
63467 63467 SRR13839969 SRX10218347 SRS8362930 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 24 hpf GSM5129557   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:24 hpf|cell type:NC cell FACS sorted NC cells 24 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:24 hpf|cell type:NC cell GSM5129557 GSM5129557: FACS sorted NC cells 24 hpf; Danio rerio; RNA Seq GSM5129557   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129557 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 24hpf S5 L001 I1 001.fastq.gz read2PairFiles=Arch 1 24hpf S5 L001 R1 001.fastq.gz read3PairFiles=Arch 1 24hpf S5 L001 R2 001.fastq.gz Arch_1_24hpf_S5_L001_I1_001.fastq.gz Arch_1_24hpf_S5_L001_R1_001.fastq.gz Arch_1_24hpf_S5_L001_R2_001.fastq.gz fastq fastq fastq 3523502928.0 26693204.0 GSM5129557 r1 0:8 1:26 2:98 A:978888790;C:774775211;G:826843137;T:941837743;N:1158047 8 26 98   978888790 774775211 826843137 941837743 1158047 SRX10218347 SRS8362930 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.92841   0.08493   0.82012   0.51404   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
63468 63468 SRR13839970 SRX10218347 SRS8362930 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 24 hpf GSM5129557   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:24 hpf|cell type:NC cell FACS sorted NC cells 24 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:24 hpf|cell type:NC cell GSM5129557 GSM5129557: FACS sorted NC cells 24 hpf; Danio rerio; RNA Seq GSM5129557   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129557 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 24hpf S6 L001 I1 001.fastq.gz read2PairFiles=Arch 1 24hpf S6 L001 R1 001.fastq.gz read3PairFiles=Arch 1 24hpf S6 L001 R2 001.fastq.gz Arch_1_24hpf_S6_L001_I1_001.fastq.gz Arch_1_24hpf_S6_L001_R1_001.fastq.gz Arch_1_24hpf_S6_L001_R2_001.fastq.gz fastq fastq fastq 2989388160.0 22646880.0 GSM5129557 r2 0:8 1:26 2:98 A:851944116;C:655854795;G:677939435;T:802666851;N:982963 8 26 98   851944116 655854795 677939435 802666851 982963 SRX10218347 SRS8362930 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.92897   0.08647   0.81781   0.51155   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
63469 63469 SRR13839971 SRX10218347 SRS8362930 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 24 hpf GSM5129557   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:24 hpf|cell type:NC cell FACS sorted NC cells 24 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:24 hpf|cell type:NC cell GSM5129557 GSM5129557: FACS sorted NC cells 24 hpf; Danio rerio; RNA Seq GSM5129557   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129557 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 24hpf S7 L001 I1 001.fastq.gz read2PairFiles=Arch 1 24hpf S7 L001 R1 001.fastq.gz read3PairFiles=Arch 1 24hpf S7 L001 R2 001.fastq.gz Arch_1_24hpf_S7_L001_I1_001.fastq.gz Arch_1_24hpf_S7_L001_R1_001.fastq.gz Arch_1_24hpf_S7_L001_R2_001.fastq.gz fastq fastq fastq 3530802792.0 26748506.0 GSM5129557 r3 0:8 1:26 2:98 A:953651270;C:750587344;G:854819839;T:970588117;N:1156222 8 26 98   953651270 750587344 854819839 970588117 1156222 SRX10218347 SRS8362930 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.93059   0.08636   0.81927   0.52426   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
63470 63470 SRR13839972 SRX10218347 SRS8362930 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 24 hpf GSM5129557   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:24 hpf|cell type:NC cell FACS sorted NC cells 24 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:24 hpf|cell type:NC cell GSM5129557 GSM5129557: FACS sorted NC cells 24 hpf; Danio rerio; RNA Seq GSM5129557   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129557 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 24hpf S8 L001 I1 001.fastq.gz read2PairFiles=Arch 1 24hpf S8 L001 R1 001.fastq.gz read3PairFiles=Arch 1 24hpf S8 L001 R2 001.fastq.gz Arch_1_24hpf_S8_L001_I1_001.fastq.gz Arch_1_24hpf_S8_L001_R1_001.fastq.gz Arch_1_24hpf_S8_L001_R2_001.fastq.gz fastq fastq fastq 3578409648.0 27109164.0 GSM5129557 r4 0:8 1:26 2:98 A:990393580;C:815778582;G:842012278;T:929057677;N:1167531 8 26 98   990393580 815778582 842012278 929057677 1167531 SRX10218347 SRS8362930 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.92935   0.08378   0.81657   0.52343   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
63471 63471 SRR13839965 SRX10218346 SRS8362929 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 20 hpf GSM5129556   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:20 hpf|cell type:NC cell FACS sorted NC cells 20 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:20 hpf|cell type:NC cell GSM5129556 GSM5129556: FACS sorted NC cells 20 hpf; Danio rerio; RNA Seq GSM5129556   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129556 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 20hpf S1 L001 I1 001.fastq.gz read2PairFiles=Arch 1 20hpf S1 L001 R1 001.fastq.gz read3PairFiles=Arch 1 20hpf S1 L001 R2 001.fastq.gz Arch_1_20hpf_S1_L001_I1_001.fastq.gz Arch_1_20hpf_S1_L001_R1_001.fastq.gz Arch_1_20hpf_S1_L001_R2_001.fastq.gz fastq fastq fastq 9657625956.0 73163833.0 GSM5129556 r1 0:8 1:26 2:98 A:2830411224;C:1999540517;G:2299090795;T:2527252325;N:1331095 8 26 98   2830411224 1999540517 2299090795 2527252325 1331095 SRX10218346 SRS8362929 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.93617   0.06368   0.82791   0.51358   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures
63472 63472 SRR13839966 SRX10218346 SRS8362929 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 20 hpf GSM5129556   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:20 hpf|cell type:NC cell FACS sorted NC cells 20 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:20 hpf|cell type:NC cell GSM5129556 GSM5129556: FACS sorted NC cells 20 hpf; Danio rerio; RNA Seq GSM5129556   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129556 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 20hpf S2 L001 I1 001.fastq.gz read2PairFiles=Arch 1 20hpf S2 L001 R1 001.fastq.gz read3PairFiles=Arch 1 20hpf S2 L001 R2 001.fastq.gz Arch_1_20hpf_S2_L001_I1_001.fastq.gz Arch_1_20hpf_S2_L001_R1_001.fastq.gz Arch_1_20hpf_S2_L001_R2_001.fastq.gz fastq fastq fastq 10865284188.0 82312759.0 GSM5129556 r2 0:8 1:26 2:98 A:2848133612;C:2502842766;G:2514230584;T:2998579778;N:1497448 8 26 98   2848133612 2502842766 2514230584 2998579778 1497448 SRX10218346 SRS8362929 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.93675   0.06269   0.82491   0.4979   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures
63473 63473 SRR13839967 SRX10218346 SRS8362929 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 20 hpf GSM5129556   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:20 hpf|cell type:NC cell FACS sorted NC cells 20 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:20 hpf|cell type:NC cell GSM5129556 GSM5129556: FACS sorted NC cells 20 hpf; Danio rerio; RNA Seq GSM5129556   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129556 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 20hpf S3 L001 I1 001.fastq.gz read2PairFiles=Arch 1 20hpf S3 L001 R1 001.fastq.gz read3PairFiles=Arch 1 20hpf S3 L001 R2 001.fastq.gz Arch_1_20hpf_S3_L001_I1_001.fastq.gz Arch_1_20hpf_S3_L001_R1_001.fastq.gz Arch_1_20hpf_S3_L001_R2_001.fastq.gz fastq fastq fastq 11483764380.0 86998215.0 GSM5129556 r3 0:8 1:26 2:98 A:3090983314;C:2570742253;G:2924510842;T:2895941869;N:1586102 8 26 98   3090983314 2570742253 2924510842 2895941869 1586102 SRX10218346 SRS8362929 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.93602   0.06124   0.82763   0.4863   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures
63474 63474 SRR13839968 SRX10218346 SRS8362929 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 20 hpf GSM5129556   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:20 hpf|cell type:NC cell FACS sorted NC cells 20 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:20 hpf|cell type:NC cell GSM5129556 GSM5129556: FACS sorted NC cells 20 hpf; Danio rerio; RNA Seq GSM5129556   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129556 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 20hpf S4 L001 I1 001.fastq.gz read2PairFiles=Arch 1 20hpf S4 L001 R1 001.fastq.gz read3PairFiles=Arch 1 20hpf S4 L001 R2 001.fastq.gz Arch_1_20hpf_S4_L001_I1_001.fastq.gz Arch_1_20hpf_S4_L001_R1_001.fastq.gz Arch_1_20hpf_S4_L001_R2_001.fastq.gz fastq fastq fastq 11921029824.0 90310832.0 GSM5129556 r4 0:8 1:26 2:98 A:3407058684;C:2744303292;G:2755684586;T:3012346092;N:1637170 8 26 98   3407058684 2744303292 2755684586 3012346092 1637170 SRX10218346 SRS8362929 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.9378   0.06268   0.82883   0.4888   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures
63475 63475 SRR13839961 SRX10218345 SRS8362927 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 18 hpf GSM5129555   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:18 hpf|cell type:NC cell FACS sorted NC cells 18 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:18 hpf|cell type:NC cell GSM5129555 GSM5129555: FACS sorted NC cells 18 hpf; Danio rerio; RNA Seq GSM5129555   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129555 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 18hpf wt S1 L002 I1 001.fastq.gz read2PairFiles=Arch 1 18hpf wt S1 L002 R1 001.fastq.gz read3PairFiles=Arch 1 18hpf wt S1 L002 R2 001.fastq.gz Arch_1_18hpf_wt_S1_L002_I1_001.fastq.gz Arch_1_18hpf_wt_S1_L002_R1_001.fastq.gz Arch_1_18hpf_wt_S1_L002_R2_001.fastq.gz fastq fastq fastq 3141297324.0 23797707.0 GSM5129555 r1 0:8 1:26 2:98 A:873609194;C:747586538;G:704993744;T:814452961;N:654887 8 26 98   873609194 747586538 704993744 814452961 654887 SRX10218345 SRS8362927 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.9322   0.08114   0.83954   0.4952   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures
63476 63476 SRR13839962 SRX10218345 SRS8362927 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 18 hpf GSM5129555   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:18 hpf|cell type:NC cell FACS sorted NC cells 18 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:18 hpf|cell type:NC cell GSM5129555 GSM5129555: FACS sorted NC cells 18 hpf; Danio rerio; RNA Seq GSM5129555   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129555 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 18hpf wt S2 L002 I1 001.fastq.gz read2PairFiles=Arch 1 18hpf wt S2 L002 R1 001.fastq.gz read3PairFiles=Arch 1 18hpf wt S2 L002 R2 001.fastq.gz Arch_1_18hpf_wt_S2_L002_I1_001.fastq.gz Arch_1_18hpf_wt_S2_L002_R1_001.fastq.gz Arch_1_18hpf_wt_S2_L002_R2_001.fastq.gz fastq fastq fastq 2127082056.0 16114258.0 GSM5129555 r2 0:8 1:26 2:98 A:570872788;C:476024398;G:493559623;T:586177888;N:447359 8 26 98   570872788 476024398 493559623 586177888 447359 SRX10218345 SRS8362927 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.93272   0.0818   0.83849   0.49119   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures
63477 63477 SRR13839963 SRX10218345 SRS8362927 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 18 hpf GSM5129555   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:18 hpf|cell type:NC cell FACS sorted NC cells 18 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:18 hpf|cell type:NC cell GSM5129555 GSM5129555: FACS sorted NC cells 18 hpf; Danio rerio; RNA Seq GSM5129555   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129555 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 18hpf wt S3 L002 I1 001.fastq.gz read2PairFiles=Arch 1 18hpf wt S3 L002 R1 001.fastq.gz read3PairFiles=Arch 1 18hpf wt S3 L002 R2 001.fastq.gz Arch_1_18hpf_wt_S3_L002_I1_001.fastq.gz Arch_1_18hpf_wt_S3_L002_R1_001.fastq.gz Arch_1_18hpf_wt_S3_L002_R2_001.fastq.gz fastq fastq fastq 879008196.0 6659153.0 GSM5129555 r3 0:8 1:26 2:98 A:254675719;C:188240134;G:200470893;T:235438920;N:182530 8 26 98   254675719 188240134 200470893 235438920 182530 SRX10218345 SRS8362927 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.92868   0.08849   0.85498   0.49912   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures
63478 63478 SRR13839964 SRX10218345 SRS8362927 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 18 hpf GSM5129555   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:18 hpf|cell type:NC cell FACS sorted NC cells 18 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:18 hpf|cell type:NC cell GSM5129555 GSM5129555: FACS sorted NC cells 18 hpf; Danio rerio; RNA Seq GSM5129555   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129555 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 18hpf wt S4 L002 I1 001.fastq.gz read2PairFiles=Arch 1 18hpf wt S4 L002 R1 001.fastq.gz read3PairFiles=Arch 1 18hpf wt S4 L002 R2 001.fastq.gz Arch_1_18hpf_wt_S4_L002_I1_001.fastq.gz Arch_1_18hpf_wt_S4_L002_R1_001.fastq.gz Arch_1_18hpf_wt_S4_L002_R2_001.fastq.gz fastq fastq fastq 2894495076.0 21927993.0 GSM5129555 r4 0:8 1:26 2:98 A:797159638;C:626294913;G:693713070;T:776722240;N:605215 8 26 98   797159638 626294913 693713070 776722240 605215 SRX10218345 SRS8362927 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.93245   0.08182   0.83615   0.48794   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures
63479 63479 SRR13839957 SRX10218344 SRS8362926 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 14 hpf GSM5129554   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:14 hpf|cell type:NC cell FACS sorted NC cells 14 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:14 hpf|cell type:NC cell GSM5129554 GSM5129554: FACS sorted NC cells 14 hpf; Danio rerio; RNA Seq GSM5129554   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129554 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 14hpf WT S1 L005 I1 001.fastq.gz read2PairFiles=Arch 1 14hpf WT S1 L005 R1 001.fastq.gz read3PairFiles=Arch 1 14hpf WT S1 L005 R2 001.fastq.gz Arch_1_14hpf_WT_S1_L005_I1_001.fastq.gz Arch_1_14hpf_WT_S1_L005_R1_001.fastq.gz Arch_1_14hpf_WT_S1_L005_R2_001.fastq.gz fastq fastq fastq 5857601244.0 44375767.0 GSM5129554 r1 0:8 1:26 2:98 A:1663829204;C:1243546230;G:1412406600;T:1536290391;N:1528819 8 26 98   1663829204 1243546230 1412406600 1536290391 1528819 SRX10218344 SRS8362926 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.9253   0.11058   0.82643   0.49122   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures
63480 63480 SRR13839958 SRX10218344 SRS8362926 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 14 hpf GSM5129554   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:14 hpf|cell type:NC cell FACS sorted NC cells 14 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:14 hpf|cell type:NC cell GSM5129554 GSM5129554: FACS sorted NC cells 14 hpf; Danio rerio; RNA Seq GSM5129554   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129554 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 14hpf WT S2 L005 I1 001.fastq.gz read2PairFiles=Arch 1 14hpf WT S2 L005 R1 001.fastq.gz read3PairFiles=Arch 1 14hpf WT S2 L005 R2 001.fastq.gz Arch_1_14hpf_WT_S2_L005_I1_001.fastq.gz Arch_1_14hpf_WT_S2_L005_R1_001.fastq.gz Arch_1_14hpf_WT_S2_L005_R2_001.fastq.gz fastq fastq fastq 4554699336.0 34505298.0 GSM5129554 r2 0:8 1:26 2:98 A:1273058982;C:927312608;G:1057773638;T:1295364329;N:1189779 8 26 98   1273058982 927312608 1057773638 1295364329 1189779 SRX10218344 SRS8362926 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.9258   0.11402   0.83364   0.50577   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures
63481 63481 SRR13839959 SRX10218344 SRS8362926 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 14 hpf GSM5129554   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:14 hpf|cell type:NC cell FACS sorted NC cells 14 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:14 hpf|cell type:NC cell GSM5129554 GSM5129554: FACS sorted NC cells 14 hpf; Danio rerio; RNA Seq GSM5129554   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129554 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 14hpf WT S3 L005 I1 001.fastq.gz read2PairFiles=Arch 1 14hpf WT S3 L005 R1 001.fastq.gz read3PairFiles=Arch 1 14hpf WT S3 L005 R2 001.fastq.gz Arch_1_14hpf_WT_S3_L005_I1_001.fastq.gz Arch_1_14hpf_WT_S3_L005_R1_001.fastq.gz Arch_1_14hpf_WT_S3_L005_R2_001.fastq.gz fastq fastq fastq 7565609832.0 57315226.0 GSM5129554 r3 0:8 1:26 2:98 A:2039815591;C:1779614574;G:1773817116;T:1970397555;N:1964996 8 26 98   2039815591 1779614574 1773817116 1970397555 1964996 SRX10218344 SRS8362926 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.92587   0.11101   0.83232   0.517   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures
63482 63482 SRR13839960 SRX10218344 SRS8362926 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 14 hpf GSM5129554   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:14 hpf|cell type:NC cell FACS sorted NC cells 14 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:14 hpf|cell type:NC cell GSM5129554 GSM5129554: FACS sorted NC cells 14 hpf; Danio rerio; RNA Seq GSM5129554   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129554 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 14hpf WT S4 L005 I1 001.fastq.gz read2PairFiles=Arch 1 14hpf WT S4 L005 R1 001.fastq.gz read3PairFiles=Arch 1 14hpf WT S4 L005 R2 001.fastq.gz Arch_1_14hpf_WT_S4_L005_I1_001.fastq.gz Arch_1_14hpf_WT_S4_L005_R1_001.fastq.gz Arch_1_14hpf_WT_S4_L005_R2_001.fastq.gz fastq fastq fastq 3957160284.0 29978487.0 GSM5129554 r4 0:8 1:26 2:98 A:1097028682;C:898797199;G:895175820;T:1065122846;N:1035737 8 26 98   1097028682 898797199 895175820 1065122846 1035737 SRX10218344 SRS8362926 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.92563   0.11323   0.82962   0.50775   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures
63483 63483 SRR13839953 SRX10218343 SRS8362928 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 12 hpf GSM5129553   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:12 hpf|cell type:NC cell FACS sorted NC cells 12 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:12 hpf|cell type:NC cell GSM5129553 GSM5129553: FACS sorted NC cells 12 hpf; Danio rerio; RNA Seq GSM5129553   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129553 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 12hpf S1 L001 I1 001.fastq.gz read2PairFiles=Arch 1 12hpf S1 L001 R1 001.fastq.gz read3PairFiles=Arch 1 12hpf S1 L001 R2 001.fastq.gz Arch_1_12hpf_S1_L001_I1_001.fastq.gz Arch_1_12hpf_S1_L001_R1_001.fastq.gz Arch_1_12hpf_S1_L001_R2_001.fastq.gz fastq fastq fastq 3226777224.0 24445282.0 GSM5129553 r1 0:8 1:26 2:98 A:952906484;C:650776912;G:768289363;T:853734570;N:1069895 8 26 98   952906484 650776912 768289363 853734570 1069895 SRX10218343 SRS8362928 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.89163   0.0998   0.84504   0.49066   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures
63484 63484 SRR13839954 SRX10218343 SRS8362928 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 12 hpf GSM5129553   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:12 hpf|cell type:NC cell FACS sorted NC cells 12 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:12 hpf|cell type:NC cell GSM5129553 GSM5129553: FACS sorted NC cells 12 hpf; Danio rerio; RNA Seq GSM5129553   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129553 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 12hpf S2 L001 I1 001.fastq.gz read2PairFiles=Arch 1 12hpf S2 L001 R1 001.fastq.gz read3PairFiles=Arch 1 12hpf S2 L001 R2 001.fastq.gz Arch_1_12hpf_S2_L001_I1_001.fastq.gz Arch_1_12hpf_S2_L001_R1_001.fastq.gz Arch_1_12hpf_S2_L001_R2_001.fastq.gz fastq fastq fastq 4997544288.0 37860184.0 GSM5129553 r2 0:8 1:26 2:98 A:1402253777;C:1125074426;G:1233125810;T:1235458619;N:1631656 8 26 98   1402253777 1125074426 1233125810 1235458619 1631656 SRX10218343 SRS8362928 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.89319   0.09696   0.84902   0.48824   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures
63485 63485 SRR13839955 SRX10218343 SRS8362928 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 12 hpf GSM5129553   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:12 hpf|cell type:NC cell FACS sorted NC cells 12 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:12 hpf|cell type:NC cell GSM5129553 GSM5129553: FACS sorted NC cells 12 hpf; Danio rerio; RNA Seq GSM5129553   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129553 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 12hpf S3 L001 I1 001.fastq.gz read2PairFiles=Arch 1 12hpf S3 L001 R1 001.fastq.gz read3PairFiles=Arch 1 12hpf S3 L001 R2 001.fastq.gz Arch_1_12hpf_S3_L001_I1_001.fastq.gz Arch_1_12hpf_S3_L001_R1_001.fastq.gz Arch_1_12hpf_S3_L001_R2_001.fastq.gz fastq fastq fastq 4544328228.0 34426729.0 GSM5129553 r3 0:8 1:26 2:98 A:1238622840;C:1020967535;G:1051847144;T:1231428502;N:1462207 8 26 98   1238622840 1020967535 1051847144 1231428502 1462207 SRX10218343 SRS8362928 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.89058   0.09671   0.84463   0.50152   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures
63486 63486 SRR13839956 SRX10218343 SRS8362928 SRP309047 PRJNA706197 scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish GSE168133 Transcriptome Analysis We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. parent bioproject:PRJNA706402 pubmed:34936864   FACS sorted NC cells 12 hpf GSM5129553   tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:12 hpf|cell type:NC cell FACS sorted NC cells 12 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. FACS sorted sox10:nEOS cells   Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   genotype:Tgsox10:nEOSw18|age:12 hpf|cell type:NC cell GSM5129553 GSM5129553: FACS sorted NC cells 12 hpf; Danio rerio; RNA Seq GSM5129553   1 Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5129553 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP309047   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 12hpf S4 L001 I1 001.fastq.gz read2PairFiles=Arch 1 12hpf S4 L001 R1 001.fastq.gz read3PairFiles=Arch 1 12hpf S4 L001 R2 001.fastq.gz Arch_1_12hpf_S4_L001_I1_001.fastq.gz Arch_1_12hpf_S4_L001_R1_001.fastq.gz Arch_1_12hpf_S4_L001_R2_001.fastq.gz fastq fastq fastq 1792708104.0 13581122.0 GSM5129553 r4 0:8 1:26 2:98 A:487946302;C:389954398;G:429068867;T:485159428;N:579109 8 26 98   487946302 389954398 429068867 485159428 579109 SRX10218343 SRS8362928 SRA1202350 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.89167   0.09552   0.84603   0.50261   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-03-03 Segmentation Embryo Embryo Imprecise All anatomical structures

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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");;