{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Larval\" and technology = \"10x\"", "rows": [[10176, "ERR5858457", "ERX5504346", "ERS6343450", "ERP128749", "PRJEB44676", "scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord", "E-MTAB-10390", "Transcriptome Analysis", "To analyse lesion induced gene regulation in progenitor cells at single cell resolution  we performed single cell RNAseq on FACS isolated her4.3:GFP progenitor cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.", "ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24", null, "Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.", "Naive", "SAMEA8658904", "University Of Edinburgh", "ENA first public:2021 05 24|ENA last update:2021 05 24|External Id:SAMEA8658904|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 05 24T00:14:32Z|INSDC last update:2021 05 24T00:14:32Z|INSDC status:public|Submitter Id:E MTAB 10390:Naive|age:4|broker name:ArrayExpress|cell type:ependymo radial glial cell|common name:zebrafish|developmental stage:larval day 4|immunophenotype:Her4.3+ positive|organism part:spinal cord|sample name:E MTAB 10390:Naive|sex:mixed|strain:WIK", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord", "E MTAB 10390:Naive p", "Naive p", "scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord", "Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.", "Experimental Factor: injury:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP128749", "Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord", "ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24", "Naive.bam", "bam", 44972162730.0, 499690697.0, "E MTAB 10390:Naive", "0:90", "A:13658826375;C:8733304343;G:9348137569;T:13228064343;N:3830100", 90, null, null, null, 13658826375, 8733304343, 9348137569, 13228064343, 3830100, "ERX5504346", "ERS6343450", "ERA4142789", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 1, 0.89428, null, 0.32693, null, 0.75276, null, 0.5314, null, 90, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2021-05-24", "Larval", "Larval", "Spinal Cord", "Nervous System"], [10177, "ERR5858456", "ERX5504345", "ERS6343449", "ERP128749", "PRJEB44676", "scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord", "E-MTAB-10390", "Transcriptome Analysis", "To analyse lesion induced gene regulation in progenitor cells at single cell resolution  we performed single cell RNAseq on FACS isolated her4.3:GFP progenitor cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.", "ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24", null, "Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.", "Lesi1d", "SAMEA8658903", "University Of Edinburgh", "ENA first public:2021 05 24|ENA last update:2021 05 24|External Id:SAMEA8658903|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 05 24T00:14:32Z|INSDC last update:2021 05 24T00:14:32Z|INSDC status:public|Submitter Id:E MTAB 10390:Lesi1d|age:4|broker name:ArrayExpress|cell type:ependymo radial glial cell|common name:zebrafish|developmental stage:larval day 4|immunophenotype:Her4.3+ positive|injury:spinal injury lesion|organism part:spinal cord|sample name:E MTAB 10390:Lesi1d|sex:mixed|strain:WIK", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord", "E MTAB 10390:Lesioned p", "Lesioned p", "scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord", "Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.", "Experimental Factor: injury:spinal injury lesion", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP128749", "Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord", "ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24", "Lesioned.bam", "bam", 49902588630.0, 554473207.0, "E MTAB 10390:Lesioned", "0:90", "A:14713351178;C:10191139050;G:10897887675;T:14095967201;N:4243526", 90, null, null, null, 14713351178, 10191139050, 10897887675, 14095967201, 4243526, "ERX5504345", "ERS6343449", "ERA4142789", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 1, 0.91197, null, 0.29137, null, 0.7568, null, 0.56523, null, 90, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2021-05-24", "Larval", "Larval", "Spinal Cord", "Nervous System"], [10186, "ERR6212423", "ERX5847531", "ERS7094943", "ERP130388", "PRJEB46176", "scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord", "E-MTAB-10379_3", "Transcriptome Analysis", "To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution  we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.", "ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08", null, "Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines", "Naive", "SAMEA9361876", "University Of Edinburgh", "ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361876|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Naive|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|organism part:spinal cord|sample name:E MTAB 10379 3:Naive|sex:mixed|strain:WIK", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord", "E MTAB 10379 3:Naive p", "Naive p", "scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord", "Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines", "Experimental Factor: injury:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP130388", "Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord", "ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08", "Mpeg_Naive_I1.fastq.gz Mpeg_Naive_R1.fastq.gz Mpeg_Naive_R2.fastq.gz", "fastq fastq fastq", 60168324125.0, 481346593.0, "E MTAB 10379 3:Naive", "0:8 1:27 2:90", "A:12424400694;C:9366563781;G:10029312355;T:11497237299;N:3679241", 8, 27, 90, null, 12424400694, 9366563781, 10029312355, 11497237299, 3679241, "ERX5847531", "ERS7094943", "ERA5186263", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 1, 0.94834, null, 0.09482, null, 0.802, null, 0.5277, null, 90, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2021-07-08", "Larval", "Larval", "Multi-tissue", "Multi-system"], [10187, "ERR6212422", "ERX5847530", "ERS7094942", "ERP130388", "PRJEB46176", "scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord", "E-MTAB-10379_3", "Transcriptome Analysis", "To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution  we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.", "ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08", null, "Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines", "Lesi1d", "SAMEA9361875", "University Of Edinburgh", "ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361875|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Lesi1d|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|injury:spinal cord lesion|organism part:spinal cord|sample name:E MTAB 10379 3:Lesi1d|sex:mixed|strain:WIK", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord", "E MTAB 10379 3:Lesioned p", "Lesioned p", "scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord", "Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines", "Experimental Factor: injury:spinal cord lesion", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP130388", "Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord", "ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08", "Mpeg_Lesioned_I1.fastq.gz Mpeg_Lesioned_R1.fastq.gz Mpeg_Lesioned_R2.fastq.gz", "fastq fastq fastq", 61701873000.0, 493614984.0, "E MTAB 10379 3:Lesioned", "0:8 1:27 2:90", "A:12952533019;C:9222397450;G:9920185920;T:12326470894;N:3761277", 8, 27, 90, null, 12952533019, 9222397450, 9920185920, 12326470894, 3761277, "ERX5847530", "ERS7094942", "ERA5186263", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 1, 0.93082, null, 0.10862, null, 0.80302, null, 0.54924, null, 90, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2021-07-08", "Larval", "Larval", "Multi-tissue", "Multi-system"], [11134, "ERR9981089", "ERX9522049", "ERS12503451", "ERP139797", "PRJEB54930", "Single cell RNA sequencing of lck GFP transgenic zebrafish", "E-MTAB-11991", "Transcriptome Analysis", "The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23", null, "Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Sample 1 lck control", "SAMEA110406305", "Institute of Environmental Medicine, Karolinska Institutet", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406305|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 1 lck control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 1 lck control|strain:Tglck:GFP", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish", "E MTAB 11991:Sample 1 lck control p", "Sample 1 lck control p", "Single cell RNA sequencing of lck GFP transgenic zebrafish", "The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0", "Experimental Factor: stimulus:n1", "AMPLICON", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP139797", "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23", "P25452_2002_S2_L001_R1_001.fastq.gz P25452_2002_S2_L001_R2_001.fastq.gz", "fastq fastq", 60177283876.0, 509976982.0, "E MTAB 11991:P25452 2002 S2 L001", "0:28 1:90", "A:17254566438;C:13547211711;G:14188233429;T:15185192817;N:2079481", 28, 90, null, null, 17254566438, 13547211711, 14188233429, 15185192817, 2079481, "ERX9522049", "ERS12503451", "ERA16488297", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", 2, 0.00671, 0.93031, 0.00231, 0.11028, 0.9932, 0.82227, 0.30887, 0.58272, 28, 90, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "full_length", "size_fractionation", "trueseq", "sc", "single_cell_droplet", "10x", null, "Sweden", "2022-07-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [11135, "ERR9981090", "ERX9522049", "ERS12503451", "ERP139797", "PRJEB54930", "Single cell RNA sequencing of lck GFP transgenic zebrafish", "E-MTAB-11991", "Transcriptome Analysis", "The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23", null, "Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Sample 1 lck control", "SAMEA110406305", "Institute of Environmental Medicine, Karolinska Institutet", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406305|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 1 lck control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 1 lck control|strain:Tglck:GFP", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish", "E MTAB 11991:Sample 1 lck control p", "Sample 1 lck control p", "Single cell RNA sequencing of lck GFP transgenic zebrafish", "The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0", "Experimental Factor: stimulus:n1", "AMPLICON", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP139797", "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23", "P25452_2002_S2_L002_R1_001.fastq.gz P25452_2002_S2_L002_R2_001.fastq.gz", "fastq fastq", 60597886144.0, 513541408.0, "E MTAB 11991:P25452 2002 S2 L002", "0:28 1:90", "A:17368154358;C:13649089056;G:14296037620;T:15282869484;N:1735626", 28, 90, null, null, 17368154358, 13649089056, 14296037620, 15282869484, 1735626, "ERX9522049", "ERS12503451", "ERA16488297", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", 2, 0.00656, 0.92899, 0.00211, 0.11059, 0.99334, 0.82335, 0.32311, 0.57644, 28, 90, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "full_length", "size_fractionation", "trueseq", "sc", "single_cell_droplet", "10x", null, "Sweden", "2022-07-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [11136, "ERR9981087", "ERX9522048", "ERS12503450", "ERP139797", "PRJEB54930", "Single cell RNA sequencing of lck GFP transgenic zebrafish", "E-MTAB-11991", "Transcriptome Analysis", "The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23", null, "Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Sample 2 lck GO+BA", "SAMEA110406304", "Institute of Environmental Medicine, Karolinska Institutet", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406304|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 2 lck GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 2 lck GO+BA|strain:Tglck:GFP", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish", "E MTAB 11991:Sample 2 lck GO+BA p", "Sample 2 lck GO+BA p", "Single cell RNA sequencing of lck GFP transgenic zebrafish", "The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Experimental Factor: stimulus:graphene oxide  30 microgram per milliliter|Experimental Factor: compound:butyrate|Experimental Factor: dose:2.5", "AMPLICON", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP139797", "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23", "P25452_2001_S1_L001_R1_001.fastq.gz P25452_2001_S1_L001_R2_001.fastq.gz", "fastq fastq", 20866120186.0, 176831527.0, "E MTAB 11991:P25452 2001 S1 L001", "0:28 1:90", "A:5933525376;C:4737179804;G:5025711080;T:5168983880;N:720046", 28, 90, null, null, 5933525376, 4737179804, 5025711080, 5168983880, 720046, "ERX9522048", "ERS12503450", "ERA16488297", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", 2, 0.00805, 0.92622, 0.00259, 0.11842, 0.99302, 0.83027, 0.2729, 0.57699, 28, 90, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "full_length", "size_fractionation", "trueseq", "sc", "single_cell_droplet", "10x", null, "Sweden", "2022-07-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [11137, "ERR9981088", "ERX9522048", "ERS12503450", "ERP139797", "PRJEB54930", "Single cell RNA sequencing of lck GFP transgenic zebrafish", "E-MTAB-11991", "Transcriptome Analysis", "The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23", null, "Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Sample 2 lck GO+BA", "SAMEA110406304", "Institute of Environmental Medicine, Karolinska Institutet", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406304|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 2 lck GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 2 lck GO+BA|strain:Tglck:GFP", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish", "E MTAB 11991:Sample 2 lck GO+BA p", "Sample 2 lck GO+BA p", "Single cell RNA sequencing of lck GFP transgenic zebrafish", "The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Experimental Factor: stimulus:graphene oxide  30 microgram per milliliter|Experimental Factor: compound:butyrate|Experimental Factor: dose:2.5", "AMPLICON", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP139797", "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish", "ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23", "P25452_2001_S1_L002_R1_001.fastq.gz P25452_2001_S1_L002_R2_001.fastq.gz", "fastq fastq", 21068682172.0, 178548154.0, "E MTAB 11991:P25452 2001 S1 L002", "0:28 1:90", "A:5987758267;C:4786100132;G:5078292970;T:5215926275;N:604528", 28, 90, null, null, 5987758267, 4786100132, 5078292970, 5215926275, 604528, "ERX9522048", "ERS12503450", "ERA16488297", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", 2, 0.00813, 0.92702, 0.00264, 0.11874, 0.99283, 0.82737, 0.30228, 0.56929, 28, 90, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "full_length", "size_fractionation", "trueseq", "sc", "single_cell_droplet", "10x", null, "Sweden", "2022-07-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [24790, "SRR25509944", "SRX21240524", "SRS18495447", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq", "GSM7680083", null, "source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680083", "GSM7680083: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680083 r1", "GSM7680083", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "5DPF_WT_plus_S17_L001_R2_001.fastq.gz 5DPF_WT_plus_S17_L001_R1_001.fastq.gz 5DPF_WT_plus_S17_L001_I1_001.fastq.gz", "fastq fastq fastq", 5999080077.0, 47236851.0, "GSM7680083 r1", "0:8 1:28 2:91", "A:1212144705;C:959823109;G:1045323833;T:1081182723;N:79071", 8, 28, 91, null, 1212144705, 959823109, 1045323833, 1081182723, 79071, "SRX21240524", "SRS18495447", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91673, null, 0.11695, null, 0.77481, null, 0.51165, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24791, "SRR25509945", "SRX21240524", "SRS18495447", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq", "GSM7680083", null, "source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680083", "GSM7680083: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680083 r1", "GSM7680083", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "5DPF_WT_plus_S17_L002_R2_001.fastq.gz 5DPF_WT_plus_S17_L002_R1_001.fastq.gz 5DPF_WT_plus_S17_L002_I1_001.fastq.gz", "fastq fastq fastq", 6012350180.0, 47341340.0, "GSM7680083 r2", "0:8 1:28 2:91", "A:1215185110;C:961739027;G:1047332997;T:1083733742;N:71064", 8, 28, 91, null, 1215185110, 961739027, 1047332997, 1083733742, 71064, "SRX21240524", "SRS18495447", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91842, null, 0.11714, null, 0.7763, null, 0.51731, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24792, "SRR25509946", "SRX21240524", "SRS18495447", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq", "GSM7680083", null, "source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680083", "GSM7680083: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680083 r1", "GSM7680083", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "5DPF_WT_plus_S18_L001_R2_001.fastq.gz 5DPF_WT_plus_S18_L001_R1_001.fastq.gz 5DPF_WT_plus_S18_L001_I1_001.fastq.gz", "fastq fastq fastq", 4990947473.0, 39298799.0, "GSM7680083 r3", "0:8 1:28 2:91", "A:1007619958;C:800073636;G:871756682;T:896670984;N:69449", 8, 28, 91, null, 1007619958, 800073636, 871756682, 896670984, 69449, "SRX21240524", "SRS18495447", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91717, null, 0.11737, null, 0.7767, null, 0.51879, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24793, "SRR25509947", "SRX21240524", "SRS18495447", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq", "GSM7680083", null, "source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680083", "GSM7680083: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680083 r1", "GSM7680083", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "5DPF_WT_plus_S18_L002_I1_001.fastq.gz 5DPF_WT_plus_S18_L002_R1_001.fastq.gz 5DPF_WT_plus_S18_L002_R2_001.fastq.gz", "fastq fastq fastq", 4994343707.0, 39325541.0, "GSM7680083 r4", "0:8 1:28 2:91", "A:1008545361;C:800479170;G:872044753;T:897494026;N:60921", 8, 28, 91, null, 1008545361, 800479170, 872044753, 897494026, 60921, "SRX21240524", "SRS18495447", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.9173, null, 0.11671, null, 0.778, null, 0.51414, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24794, "SRR25509948", "SRX21240524", "SRS18495447", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq", "GSM7680083", null, "source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680083", "GSM7680083: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680083 r1", "GSM7680083", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "5DPF_WT_plus_S20_L001_R2_001.fastq.gz 5DPF_WT_plus_S20_L001_R1_001.fastq.gz 5DPF_WT_plus_S20_L001_I1_001.fastq.gz", "fastq fastq fastq", 4150807675.0, 32683525.0, "GSM7680083 r7", "0:8 1:28 2:91", "A:839301254;C:665476121;G:723277159;T:746089009;N:57232", 8, 28, 91, null, 839301254, 665476121, 723277159, 746089009, 57232, "SRX21240524", "SRS18495447", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91704, null, 0.11665, null, 0.77589, null, 0.51231, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24795, "SRR25509949", "SRX21240524", "SRS18495447", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq", "GSM7680083", null, "source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680083", "GSM7680083: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680083 r1", "GSM7680083", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "5DPF_WT_plus_S20_L002_R2_001.fastq.gz 5DPF_WT_plus_S20_L002_R1_001.fastq.gz 5DPF_WT_plus_S20_L002_I1_001.fastq.gz", "fastq fastq fastq", 4152701499.0, 32698437.0, "GSM7680083 r8", "0:8 1:28 2:91", "A:839837413;C:665793367;G:723399518;T:746476220;N:51249", 8, 28, 91, null, 839837413, 665793367, 723399518, 746476220, 51249, "SRX21240524", "SRS18495447", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91769, null, 0.11677, null, 0.77473, null, 0.5172, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24796, "SRR25510006", "SRX21240524", "SRS18495447", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq", "GSM7680083", null, "source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680083", "GSM7680083: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680083 r1", "GSM7680083", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "5DPF_WT_plus_S19_L001_I1_001.fastq.gz 5DPF_WT_plus_S19_L001_R1_001.fastq.gz 5DPF_WT_plus_S19_L001_R2_001.fastq.gz", "fastq fastq fastq", 5570139228.0, 43859364.0, "GSM7680083 r5", "0:8 1:28 2:91", "A:1124433319;C:892106407;G:974065175;T:1000519772;N:77451", 8, 28, 91, null, 1124433319, 892106407, 974065175, 1000519772, 77451, "SRX21240524", "SRS18495447", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.9181, null, 0.11708, null, 0.77725, null, 0.506, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24797, "SRR25510007", "SRX21240524", "SRS18495447", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq", "GSM7680083", null, "source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680083", "GSM7680083: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680083 r1", "GSM7680083", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "5DPF_WT_plus_S19_L002_R2_001.fastq.gz 5DPF_WT_plus_S19_L002_R1_001.fastq.gz 5DPF_WT_plus_S19_L002_I1_001.fastq.gz", "fastq fastq fastq", 5568879134.0, 43849442.0, "GSM7680083 r6", "0:8 1:28 2:91", "A:1124462080;C:891765530;G:973382320;T:1000621312;N:67980", 8, 28, 91, null, 1124462080, 891765530, 973382320, 1000621312, 67980, "SRX21240524", "SRS18495447", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91836, null, 0.11752, null, 0.77786, null, 0.49118, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24798, "SRR25509950", "SRX21240523", "SRS18495446", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq", "GSM7680088", null, "source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680088", "GSM7680088: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680088 r1", "GSM7680088", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "MECOM_minus_S29_L001_I1_001.fastq.gz MECOM_minus_S29_L001_R1_001.fastq.gz MECOM_minus_S29_L001_R2_001.fastq.gz", "fastq fastq fastq", 6472457718.0, 50964234.0, "GSM7680088 r1", "0:8 1:28 2:91", "A:1374177983;C:969847712;G:1063043909;T:1230585953;N:89737", 8, 28, 91, null, 1374177983, 969847712, 1063043909, 1230585953, 89737, "SRX21240523", "SRS18495446", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91899, null, 0.23002, null, 0.75597, null, 0.50918, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24799, "SRR25509951", "SRX21240523", "SRS18495446", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq", "GSM7680088", null, "source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680088", "GSM7680088: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680088 r1", "GSM7680088", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "MECOM_minus_S29_L002_I1_001.fastq.gz MECOM_minus_S29_L002_R1_001.fastq.gz MECOM_minus_S29_L002_R2_001.fastq.gz", "fastq fastq fastq", 6479801747.0, 51022061.0, "GSM7680088 r2", "0:8 1:28 2:91", "A:1375879660;C:970771702;G:1064110805;T:1232166662;N:78722", 8, 28, 91, null, 1375879660, 970771702, 1064110805, 1232166662, 78722, "SRX21240523", "SRS18495446", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91932, null, 0.23011, null, 0.75666, null, 0.50726, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24800, "SRR25509952", "SRX21240523", "SRS18495446", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq", "GSM7680088", null, "source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680088", "GSM7680088: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680088 r1", "GSM7680088", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "MECOM_minus_S30_L001_I1_001.fastq.gz MECOM_minus_S30_L001_R1_001.fastq.gz MECOM_minus_S30_L001_R2_001.fastq.gz", "fastq fastq fastq", 6055044278.0, 47677514.0, "GSM7680088 r3", "0:8 1:28 2:91", "A:1285162347;C:907248700;G:995411468;T:1150745942;N:85317", 8, 28, 91, null, 1285162347, 907248700, 995411468, 1150745942, 85317, "SRX21240523", "SRS18495446", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91771, null, 0.2306, null, 0.75799, null, 0.51641, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24801, "SRR25509953", "SRX21240523", "SRS18495446", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq", "GSM7680088", null, "source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680088", "GSM7680088: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680088 r1", "GSM7680088", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "MECOM_minus_S30_L002_I1_001.fastq.gz MECOM_minus_S30_L002_R1_001.fastq.gz MECOM_minus_S30_L002_R2_001.fastq.gz", "fastq fastq fastq", 6065969453.0, 47763539.0, "GSM7680088 r4", "0:8 1:28 2:91", "A:1287814805;C:908939739;G:996849881;T:1152803356;N:74268", 8, 28, 91, null, 1287814805, 908939739, 996849881, 1152803356, 74268, "SRX21240523", "SRS18495446", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91856, null, 0.23244, null, 0.75844, null, 0.51273, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24802, "SRR25509954", "SRX21240523", "SRS18495446", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq", "GSM7680088", null, "source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680088", "GSM7680088: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680088 r1", "GSM7680088", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "MECOM_minus_S31_L001_I1_001.fastq.gz MECOM_minus_S31_L001_R1_001.fastq.gz MECOM_minus_S31_L001_R2_001.fastq.gz", "fastq fastq fastq", 5279309101.0, 41569363.0, "GSM7680088 r5", "0:8 1:28 2:91", "A:1122213686;C:789300425;G:868235888;T:1002988275;N:73759", 8, 28, 91, null, 1122213686, 789300425, 868235888, 1002988275, 73759, "SRX21240523", "SRS18495446", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91638, null, 0.23107, null, 0.75795, null, 0.51508, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24803, "SRR25509955", "SRX21240523", "SRS18495446", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq", "GSM7680088", null, "source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680088", "GSM7680088: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680088 r1", "GSM7680088", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "MECOM_minus_S31_L002_I1_001.fastq.gz MECOM_minus_S31_L002_R1_001.fastq.gz MECOM_minus_S31_L002_R2_001.fastq.gz", "fastq fastq fastq", 5282579605.0, 41595115.0, "GSM7680088 r6", "0:8 1:28 2:91", "A:1123052612;C:789776127;G:868371205;T:1003891470;N:64051", 8, 28, 91, null, 1123052612, 789776127, 868371205, 1003891470, 64051, "SRX21240523", "SRS18495446", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91687, null, 0.23155, null, 0.75653, null, 0.51167, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24804, "SRR25509956", "SRX21240523", "SRS18495446", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq", "GSM7680088", null, "source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680088", "GSM7680088: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680088 r1", "GSM7680088", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "MECOM_minus_S32_L001_I1_001.fastq.gz MECOM_minus_S32_L001_R1_001.fastq.gz MECOM_minus_S32_L001_R2_001.fastq.gz", "fastq fastq fastq", 5155833986.0, 40597118.0, "GSM7680088 r7", "0:8 1:28 2:91", "A:1096166065;C:771837218;G:846468036;T:979794053;N:72366", 8, 28, 91, null, 1096166065, 771837218, 846468036, 979794053, 72366, "SRX21240523", "SRS18495446", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91864, null, 0.23062, null, 0.75783, null, 0.5144, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24805, "SRR25509957", "SRX21240523", "SRS18495446", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq", "GSM7680088", null, "source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680088", "GSM7680088: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680088 r1", "GSM7680088", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "MECOM_minus_S32_L002_I1_001.fastq.gz MECOM_minus_S32_L002_R1_001.fastq.gz MECOM_minus_S32_L002_R2_001.fastq.gz", "fastq fastq fastq", 5158852395.0, 40620885.0, "GSM7680088 r8", "0:8 1:28 2:91", "A:1096925078;C:772260867;G:846795917;T:980455576;N:63097", 8, 28, 91, null, 1096925078, 772260867, 846795917, 980455576, 63097, "SRX21240523", "SRS18495446", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91859, null, 0.23143, null, 0.75921, null, 0.51192, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24806, "SRR25509958", "SRX21240522", "SRS18495445", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq", "GSM7680087", null, "source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680087", "GSM7680087: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680087 r1", "GSM7680087", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "PRDM16-GFP_S1_L001_I1_001.fastq.gz PRDM16-GFP_S1_L001_R1_001.fastq.gz PRDM16-GFP_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 7339736654.0, 57793202.0, "GSM7680087 r1", "0:8 1:28 2:91", "A:1557377528;C:1077119414;G:1156228317;T:1468352980;N:103143", 8, 28, 91, null, 1557377528, 1077119414, 1156228317, 1468352980, 103143, "SRX21240522", "SRS18495445", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91516, null, 0.25902, null, 0.74255, null, 0.49922, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24807, "SRR25509959", "SRX21240522", "SRS18495445", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq", "GSM7680087", null, "source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680087", "GSM7680087: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680087 r1", "GSM7680087", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "PRDM16-GFP_S1_L002_I1_001.fastq.gz PRDM16-GFP_S1_L002_R1_001.fastq.gz PRDM16-GFP_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 7410090336.0, 58347168.0, "GSM7680087 r2", "0:8 1:28 2:91", "A:1569421640;C:1090998538;G:1171253819;T:1477822651;N:95640", 8, 28, 91, null, 1569421640, 1090998538, 1171253819, 1477822651, 95640, "SRX21240522", "SRS18495445", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91462, null, 0.25846, null, 0.74215, null, 0.49672, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24808, "SRR25509960", "SRX21240522", "SRS18495445", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq", "GSM7680087", null, "source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680087", "GSM7680087: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680087 r1", "GSM7680087", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "PRDM16-GFP_S2_L001_I1_001.fastq.gz PRDM16-GFP_S2_L001_R1_001.fastq.gz PRDM16-GFP_S2_L001_R2_001.fastq.gz", "fastq fastq fastq", 7620847217.0, 60006671.0, "GSM7680087 r3", "0:8 1:28 2:91", "A:1615026295;C:1121044318;G:1201364994;T:1523062938;N:108516", 8, 28, 91, null, 1615026295, 1121044318, 1201364994, 1523062938, 108516, "SRX21240522", "SRS18495445", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91495, null, 0.26021, null, 0.74188, null, 0.49871, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24809, "SRR25509961", "SRX21240522", "SRS18495445", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq", "GSM7680087", null, "source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680087", "GSM7680087: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680087 r1", "GSM7680087", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "PRDM16-GFP_S2_L002_I1_001.fastq.gz PRDM16-GFP_S2_L002_R1_001.fastq.gz PRDM16-GFP_S2_L002_R2_001.fastq.gz", "fastq fastq fastq", 7658170739.0, 60300557.0, "GSM7680087 r4", "0:8 1:28 2:91", "A:1620018228;C:1130072970;G:1211145212;T:1526013817;N:100460", 8, 28, 91, null, 1620018228, 1130072970, 1211145212, 1526013817, 100460, "SRX21240522", "SRS18495445", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.9153, null, 0.25733, null, 0.74406, null, 0.49822, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24810, "SRR25509962", "SRX21240522", "SRS18495445", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq", "GSM7680087", null, "source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680087", "GSM7680087: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680087 r1", "GSM7680087", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "PRDM16-GFP_S3_L001_I1_001.fastq.gz PRDM16-GFP_S3_L001_R1_001.fastq.gz PRDM16-GFP_S3_L001_R2_001.fastq.gz", "fastq fastq fastq", 7520150568.0, 59213784.0, "GSM7680087 r5", "0:8 1:28 2:91", "A:1592224470;C:1104917106;G:1187483622;T:1503722424;N:106722", 8, 28, 91, null, 1592224470, 1104917106, 1187483622, 1503722424, 106722, "SRX21240522", "SRS18495445", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91528, null, 0.25852, null, 0.74168, null, 0.50087, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24811, "SRR25509963", "SRX21240522", "SRS18495445", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq", "GSM7680087", null, "source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680087", "GSM7680087: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680087 r1", "GSM7680087", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "PRDM16-GFP_S3_L002_I1_001.fastq.gz PRDM16-GFP_S3_L002_R1_001.fastq.gz PRDM16-GFP_S3_L002_R2_001.fastq.gz", "fastq fastq fastq", 7547416198.0, 59428474.0, "GSM7680087 r6", "0:8 1:28 2:91", "A:1595335949;C:1112405532;G:1195632258;T:1504519719;N:97676", 8, 28, 91, null, 1595335949, 1112405532, 1195632258, 1504519719, 97676, "SRX21240522", "SRS18495445", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91572, null, 0.25684, null, 0.74227, null, 0.49429, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24812, "SRR25509964", "SRX21240522", "SRS18495445", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq", "GSM7680087", null, "source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680087", "GSM7680087: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680087 r1", "GSM7680087", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "PRDM16-GFP_S4_L001_I1_001.fastq.gz PRDM16-GFP_S4_L001_R1_001.fastq.gz PRDM16-GFP_S4_L001_R2_001.fastq.gz", "fastq fastq fastq", 6203887389.0, 48849507.0, "GSM7680087 r7", "0:8 1:28 2:91", "A:1315023626;C:910416020;G:979167464;T:1240610297;N:87730", 8, 28, 91, null, 1315023626, 910416020, 979167464, 1240610297, 87730, "SRX21240522", "SRS18495445", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91294, null, 0.25905, null, 0.74426, null, 0.49642, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24813, "SRR25509965", "SRX21240522", "SRS18495445", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq", "GSM7680087", null, "source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680087", "GSM7680087: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680087 r1", "GSM7680087", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "PRDM16-GFP_S4_L002_I1_001.fastq.gz PRDM16-GFP_S4_L002_R1_001.fastq.gz PRDM16-GFP_S4_L002_R2_001.fastq.gz", "fastq fastq fastq", 6164249419.0, 48537397.0, "GSM7680087 r8", "0:8 1:28 2:91", "A:1303982345;C:907803673;G:976227040;T:1228810005;N:80064", 8, 28, 91, null, 1303982345, 907803673, 976227040, 1228810005, 80064, "SRX21240522", "SRS18495445", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91422, null, 0.25666, null, 0.74383, null, 0.49596, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24814, "SRR25509966", "SRX21240521", "SRS18495444", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq", "GSM7680086", null, "source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680086", "GSM7680086: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680086 r1", "GSM7680086", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "MECOM_plus_S25_L001_I1_001.fastq.gz MECOM_plus_S25_L001_R1_001.fastq.gz MECOM_plus_S25_L001_R2_001.fastq.gz", "fastq fastq fastq", 2154821446.0, 16967098.0, "GSM7680086 r1", "0:8 1:28 2:91", "A:451330902;C:339756831;G:379343350;T:373544930;N:29905", 8, 28, 91, null, 451330902, 339756831, 379343350, 373544930, 29905, "SRX21240521", "SRS18495444", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91882, null, 0.142, null, 0.78299, null, 0.51956, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24815, "SRR25509967", "SRX21240521", "SRS18495444", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq", "GSM7680086", null, "source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680086", "GSM7680086: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680086 r1", "GSM7680086", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "MECOM_plus_S25_L002_I1_001.fastq.gz MECOM_plus_S25_L002_R1_001.fastq.gz MECOM_plus_S25_L002_R2_001.fastq.gz", "fastq fastq fastq", 2158219204.0, 16993852.0, "GSM7680086 r2", "0:8 1:28 2:91", "A:452280625;C:340228509;G:379707034;T:374197697;N:26667", 8, 28, 91, null, 452280625, 340228509, 379707034, 374197697, 26667, "SRX21240521", "SRS18495444", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91895, null, 0.1417, null, 0.78279, null, 0.51981, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24816, "SRR25509968", "SRX21240521", "SRS18495444", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq", "GSM7680086", null, "source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680086", "GSM7680086: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680086 r1", "GSM7680086", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "MECOM_plus_S26_L001_I1_001.fastq.gz MECOM_plus_S26_L001_R1_001.fastq.gz MECOM_plus_S26_L001_R2_001.fastq.gz", "fastq fastq fastq", 2361287251.0, 18592813.0, "GSM7680086 r3", "0:8 1:28 2:91", "A:492891294;C:373079069;G:416862992;T:409079819;N:32809", 8, 28, 91, null, 492891294, 373079069, 416862992, 409079819, 32809, "SRX21240521", "SRS18495444", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.92068, null, 0.13997, null, 0.78516, null, 0.50532, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24817, "SRR25509969", "SRX21240521", "SRS18495444", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq", "GSM7680086", null, "source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680086", "GSM7680086: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680086 r1", "GSM7680086", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "MECOM_plus_S26_L002_I1_001.fastq.gz MECOM_plus_S26_L002_R1_001.fastq.gz MECOM_plus_S26_L002_R2_001.fastq.gz", "fastq fastq fastq", 2362115545.0, 18599335.0, "GSM7680086 r4", "0:8 1:28 2:91", "A:493282758;C:373220256;G:416785305;T:409222388;N:28778", 8, 28, 91, null, 493282758, 373220256, 416785305, 409222388, 28778, "SRX21240521", "SRS18495444", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.92013, null, 0.14129, null, 0.78468, null, 0.52049, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24818, "SRR25509970", "SRX21240521", "SRS18495444", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq", "GSM7680086", null, "source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680086", "GSM7680086: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680086 r1", "GSM7680086", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "MECOM_plus_S27_L001_I1_001.fastq.gz MECOM_plus_S27_L001_R1_001.fastq.gz MECOM_plus_S27_L001_R2_001.fastq.gz", "fastq fastq fastq", 2093107066.0, 16481158.0, "GSM7680086 r5", "0:8 1:28 2:91", "A:438295698;C:330083473;G:369094473;T:362282989;N:28745", 8, 28, 91, null, 438295698, 330083473, 369094473, 362282989, 28745, "SRX21240521", "SRS18495444", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91759, null, 0.13991, null, 0.78354, null, 0.51917, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24819, "SRR25509971", "SRX21240521", "SRS18495444", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq", "GSM7680086", null, "source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680086", "GSM7680086: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680086 r1", "GSM7680086", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "MECOM_plus_S27_L002_R2_001.fastq.gz MECOM_plus_S27_L002_R1_001.fastq.gz MECOM_plus_S27_L002_I1_001.fastq.gz", "fastq fastq fastq", 2095025401.0, 16496263.0, "GSM7680086 r6", "0:8 1:28 2:91", "A:438926470;C:330300198;G:369243520;T:362664613;N:25132", 8, 28, 91, null, 438926470, 330300198, 369243520, 362664613, 25132, "SRX21240521", "SRS18495444", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91795, null, 0.14216, null, 0.78151, null, 0.5067, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24820, "SRR25509972", "SRX21240521", "SRS18495444", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq", "GSM7680086", null, "source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680086", "GSM7680086: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680086 r1", "GSM7680086", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "MECOM_plus_S28_L001_R2_001.fastq.gz MECOM_plus_S28_L001_R1_001.fastq.gz MECOM_plus_S28_L001_I1_001.fastq.gz", "fastq fastq fastq", 1722573390.0, 13563570.0, "GSM7680086 r7", "0:8 1:28 2:91", "A:360865837;C:272246731;G:303643951;T:297504190;N:24161", 8, 28, 91, null, 360865837, 272246731, 303643951, 297504190, 24161, "SRX21240521", "SRS18495444", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91897, null, 0.13999, null, 0.78648, null, 0.49913, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24821, "SRR25509973", "SRX21240521", "SRS18495444", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq", "GSM7680086", null, "source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680086", "GSM7680086: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680086 r1", "GSM7680086", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "MECOM_plus_S28_L002_I1_001.fastq.gz MECOM_plus_S28_L002_R1_001.fastq.gz MECOM_plus_S28_L002_R2_001.fastq.gz", "fastq fastq fastq", 1724036303.0, 13575089.0, "GSM7680086 r8", "0:8 1:28 2:91", "A:361391368;C:272402118;G:303699423;T:297819212;N:20978", 8, 28, 91, null, 361391368, 272402118, 303699423, 297819212, 20978, "SRX21240521", "SRS18495444", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.92182, null, 0.14094, null, 0.78326, null, 0.50699, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24822, "SRR25509974", "SRX21240520", "SRS18495443", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq", "GSM7680085", null, "source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680085", "GSM7680085: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680085 r1", "GSM7680085", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "PRDM16plusGFP_S5_L001_R2_001.fastq.gz PRDM16plusGFP_S5_L001_R1_001.fastq.gz PRDM16plusGFP_S5_L001_I1_001.fastq.gz", "fastq fastq fastq", 8567717053.0, 67462339.0, "GSM7680085 r1", "0:8 1:28 2:91", "A:1758073165;C:1341216272;G:1446728174;T:1592934812;N:120426", 8, 28, 91, null, 1758073165, 1341216272, 1446728174, 1592934812, 120426, "SRX21240520", "SRS18495443", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.90663, null, 0.17669, null, 0.75812, null, 0.50234, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24823, "SRR25509975", "SRX21240520", "SRS18495443", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq", "GSM7680085", null, "source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680085", "GSM7680085: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680085 r1", "GSM7680085", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "PRDM16plusGFP_S5_L002_R2_001.fastq.gz PRDM16plusGFP_S5_L002_R1_001.fastq.gz PRDM16plusGFP_S5_L002_I1_001.fastq.gz", "fastq fastq fastq", 8694310526.0, 68459138.0, "GSM7680085 r2", "0:8 1:28 2:91", "A:1780912602;C:1365177337;G:1472402153;T:1611176829;N:112637", 8, 28, 91, null, 1780912602, 1365177337, 1472402153, 1611176829, 112637, "SRX21240520", "SRS18495443", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.90543, null, 0.17508, null, 0.76019, null, 0.51005, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24824, "SRR25509976", "SRX21240520", "SRS18495443", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq", "GSM7680085", null, "source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680085", "GSM7680085: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680085 r1", "GSM7680085", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "PRDM16plusGFP_S6_L001_R2_001.fastq.gz PRDM16plusGFP_S6_L001_R1_001.fastq.gz PRDM16plusGFP_S6_L001_I1_001.fastq.gz", "fastq fastq fastq", 9112215456.0, 71749728.0, "GSM7680085 r3", "0:8 1:28 2:91", "A:1868388882;C:1426817380;G:1540502920;T:1693385950;N:130116", 8, 28, 91, null, 1868388882, 1426817380, 1540502920, 1693385950, 130116, "SRX21240520", "SRS18495443", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.90763, null, 0.17756, null, 0.76102, null, 0.50457, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24825, "SRR25509977", "SRX21240520", "SRS18495443", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq", "GSM7680085", null, "source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680085", "GSM7680085: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680085 r1", "GSM7680085", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "PRDM16plusGFP_S6_L002_I1_001.fastq.gz PRDM16plusGFP_S6_L002_R1_001.fastq.gz PRDM16plusGFP_S6_L002_R2_001.fastq.gz", "fastq fastq fastq", 9170568781.0, 72209203.0, "GSM7680085 r4", "0:8 1:28 2:91", "A:1876786596;C:1440704341;G:1555176461;T:1698251178;N:118897", 8, 28, 91, null, 1876786596, 1440704341, 1555176461, 1698251178, 118897, "SRX21240520", "SRS18495443", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.9062, null, 0.17617, null, 0.76203, null, 0.49732, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24826, "SRR25509978", "SRX21240520", "SRS18495443", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq", "GSM7680085", null, "source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680085", "GSM7680085: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680085 r1", "GSM7680085", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "PRDM16plusGFP_S7_L001_R2_001.fastq.gz PRDM16plusGFP_S7_L001_R1_001.fastq.gz PRDM16plusGFP_S7_L001_I1_001.fastq.gz", "fastq fastq fastq", 96282510.0, 758130.0, "GSM7680085 r5", "0:8 1:28 2:91", "A:19884451;C:15070058;G:16206702;T:17827293;N:1326", 8, 28, 91, null, 19884451, 15070058, 16206702, 17827293, 1326, "SRX21240520", "SRS18495443", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.76071, null, 0.14671, null, 0.78064, null, 0.49267, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24827, "SRR25509979", "SRX21240520", "SRS18495443", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq", "GSM7680085", null, "source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680085", "GSM7680085: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680085 r1", "GSM7680085", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "PRDM16plusGFP_S7_L002_I1_001.fastq.gz PRDM16plusGFP_S7_L002_R2_001.fastq.gz PRDM16plusGFP_S7_L002_R1_001.fastq.gz", "fastq fastq fastq", 96503236.0, 759868.0, "GSM7680085 r6", "0:8 1:28 2:91", "A:19898524;C:15152212;G:16290226;T:17805918;N:1108", 8, 28, 91, null, 19898524, 15152212, 16290226, 17805918, 1108, "SRX21240520", "SRS18495443", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.76382, null, 0.1467, null, 0.78508, null, 0.48995, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24828, "SRR25509980", "SRX21240520", "SRS18495443", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq", "GSM7680085", null, "source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680085", "GSM7680085: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680085 r1", "GSM7680085", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "PRDM16plusGFP_S8_L001_I1_001.fastq.gz PRDM16plusGFP_S8_L001_R1_001.fastq.gz PRDM16plusGFP_S8_L001_R2_001.fastq.gz", "fastq fastq fastq", 8873313978.0, 69868614.0, "GSM7680085 r7", "0:8 1:28 2:91", "A:1820893372;C:1390912026;G:1498935631;T:1647176605;N:126240", 8, 28, 91, null, 1820893372, 1390912026, 1498935631, 1647176605, 126240, "SRX21240520", "SRS18495443", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.90718, null, 0.17603, null, 0.76211, null, 0.50458, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24829, "SRR25509981", "SRX21240520", "SRS18495443", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq", "GSM7680085", null, "source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680085", "GSM7680085: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680085 r1", "GSM7680085", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "PRDM16plusGFP_S8_L002_I1_001.fastq.gz PRDM16plusGFP_S8_L002_R1_001.fastq.gz PRDM16plusGFP_S8_L002_R2_001.fastq.gz", "fastq fastq fastq", 8980314526.0, 70711138.0, "GSM7680085 r8", "0:8 1:28 2:91", "A:1839681468;C:1412028536;G:1521396962;T:1661490212;N:116380", 8, 28, 91, null, 1839681468, 1412028536, 1521396962, 1661490212, 116380, "SRX21240520", "SRS18495443", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.9078, null, 0.17604, null, 0.76037, null, 0.47729, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24830, "SRR25509982", "SRX21240519", "SRS18495442", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq", "GSM7680084", null, "source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680084", "GSM7680084: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680084 r1", "GSM7680084", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "5DPF_WT_minus_S21_L001_I1_001.fastq.gz 5DPF_WT_minus_S21_L001_R1_001.fastq.gz 5DPF_WT_minus_S21_L001_R2_001.fastq.gz", "fastq fastq fastq", 8634577600.0, 67988800.0, "GSM7680084 r1", "0:8 1:28 2:91", "A:1833391508;C:1279550998;G:1408086737;T:1665829499;N:122058", 8, 28, 91, null, 1833391508, 1279550998, 1408086737, 1665829499, 122058, "SRX21240519", "SRS18495442", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.92, null, 0.2485, null, 0.75552, null, 0.51753, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24831, "SRR25509983", "SRX21240519", "SRS18495442", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq", "GSM7680084", null, "source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680084", "GSM7680084: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680084 r1", "GSM7680084", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "5DPF_WT_minus_S21_L002_I1_001.fastq.gz 5DPF_WT_minus_S21_L002_R1_001.fastq.gz 5DPF_WT_minus_S21_L002_R2_001.fastq.gz", "fastq fastq fastq", 8644279892.0, 68065196.0, "GSM7680084 r2", "0:8 1:28 2:91", "A:1835831383;C:1280886675;G:1409188624;T:1667919807;N:106347", 8, 28, 91, null, 1835831383, 1280886675, 1409188624, 1667919807, 106347, "SRX21240519", "SRS18495442", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91942, null, 0.24867, null, 0.75396, null, 0.52058, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24832, "SRR25509984", "SRX21240519", "SRS18495442", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq", "GSM7680084", null, "source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680084", "GSM7680084: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680084 r1", "GSM7680084", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "5DPF_WT_minus_S22_L001_R2_001.fastq.gz 5DPF_WT_minus_S22_L001_R1_001.fastq.gz 5DPF_WT_minus_S22_L001_I1_001.fastq.gz", "fastq fastq fastq", 6144243998.0, 48379874.0, "GSM7680084 r3", "0:8 1:28 2:91", "A:1307018689;C:910675193;G:999334562;T:1185454346;N:85744", 8, 28, 91, null, 1307018689, 910675193, 999334562, 1185454346, 85744, "SRX21240519", "SRS18495442", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91944, null, 0.2505, null, 0.75538, null, 0.5154, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24833, "SRR25509985", "SRX21240519", "SRS18495442", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq", "GSM7680084", null, "source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680084", "GSM7680084: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680084 r1", "GSM7680084", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "5DPF_WT_minus_S22_L002_I1_001.fastq.gz 5DPF_WT_minus_S22_L002_R1_001.fastq.gz 5DPF_WT_minus_S22_L002_R2_001.fastq.gz", "fastq fastq fastq", 6161162938.0, 48513094.0, "GSM7680084 r4", "0:8 1:28 2:91", "A:1310818438;C:913067206;G:1001801994;T:1188928241;N:75675", 8, 28, 91, null, 1310818438, 913067206, 1001801994, 1188928241, 75675, "SRX21240519", "SRS18495442", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91847, null, 0.24895, null, 0.75483, null, 0.52092, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24834, "SRR25509986", "SRX21240519", "SRS18495442", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq", "GSM7680084", null, "source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680084", "GSM7680084: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680084 r1", "GSM7680084", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "5DPF_WT_minus_S23_L001_I1_001.fastq.gz 5DPF_WT_minus_S23_L001_R1_001.fastq.gz 5DPF_WT_minus_S23_L001_R2_001.fastq.gz", "fastq fastq fastq", 6893652075.0, 54280725.0, "GSM7680084 r5", "0:8 1:28 2:91", "A:1466387768;C:1021460104;G:1123606745;T:1327994370;N:96988", 8, 28, 91, null, 1466387768, 1021460104, 1123606745, 1327994370, 96988, "SRX21240519", "SRS18495442", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.92042, null, 0.24759, null, 0.75663, null, 0.51662, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24835, "SRR25509987", "SRX21240519", "SRS18495442", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq", "GSM7680084", null, "source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680084", "GSM7680084: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680084 r1", "GSM7680084", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "5DPF_WT_minus_S23_L002_R1_001.fastq.gz 5DPF_WT_minus_S23_L002_R2_001.fastq.gz 5DPF_WT_minus_S23_L002_I1_001.fastq.gz", "fastq fastq fastq", 6907881409.0, 54392767.0, "GSM7680084 r6", "0:8 1:28 2:91", "A:1469526451;C:1023529399;G:1125771813;T:1330830542;N:83592", 8, 28, 91, null, 1469526451, 1023529399, 1125771813, 1330830542, 83592, "SRX21240519", "SRS18495442", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91879, null, 0.24904, null, 0.75479, null, 0.52175, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24836, "SRR25509988", "SRX21240519", "SRS18495442", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq", "GSM7680084", null, "source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680084", "GSM7680084: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680084 r1", "GSM7680084", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "5DPF_WT_minus_S24_L001_R2_001.fastq.gz 5DPF_WT_minus_S24_L001_R1_001.fastq.gz 5DPF_WT_minus_S24_L001_I1_001.fastq.gz", "fastq fastq fastq", 6155284362.0, 48466806.0, "GSM7680084 r7", "0:8 1:28 2:91", "A:1309788155;C:909805561;G:1001863122;T:1188939208;N:83300", 8, 28, 91, null, 1309788155, 909805561, 1001863122, 1188939208, 83300, "SRX21240519", "SRS18495442", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91932, null, 0.252, null, 0.7541, null, 0.52096, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [24837, "SRR25509989", "SRX21240519", "SRS18495442", "SRP453227", "PRJNA1001940", "Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed", "GSE240026", "Transcriptome Analysis", "Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.", null, "pubmed:37676768", null, "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq", "GSM7680084", null, "source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing", "Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files", "tail", null, "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs", "GSM7680084", "GSM7680084: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq; Danio rerio; RNA Seq", "GSM7680084 r1", "GSM7680084", "1", "DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453227", null, "loader:fastq load.py", "5DPF_WT_minus_S24_L002_I1_001.fastq.gz 5DPF_WT_minus_S24_L002_R1_001.fastq.gz 5DPF_WT_minus_S24_L002_R2_001.fastq.gz", "fastq fastq fastq", 6165991605.0, 48551115.0, "GSM7680084 r8", "0:8 1:28 2:91", "A:1312424825;C:911081786;G:1003163970;T:1191408145;N:72739", 8, 28, 91, null, 1312424825, 911081786, 1003163970, 1191408145, 72739, "SRX21240519", "SRS18495442", "SRA1686067", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", "Dasen, Neuroscience Institute, New York University Grossman School of Medicine", 1, 0.91842, null, 0.24989, null, 0.75542, null, 0.51918, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-03", "Larval", "Larval", "Tail", "Multi-system"], [25237, "SRR25721801", "SRX21445937", "SRS18680715", "SRP456253", "PRJNA1007646", "Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival [larva]", "GSE241296", "Other", "Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish  this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation  making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however  the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach  we demonstrate that larval RBs in zebrafish fall into three  largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities  including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover  this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib  which is used in clinic and causes peripheral neuropathy. Importantly  dovitinib mediated axon loss can be suppressed by loss of Sarm1  a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 \u00b0C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 \u00b5m respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 \u00b0C for 25 min. The digestion was terminated by adding 500 \u00b5l stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4\u00b0C  washed once with L15 and resuspended in 200 \u00b5l of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 \u00b5m opening. The solution was filtered through a 35 \u00b5m strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing", null, null, null, "zebrafish larva  neurons and glia  scRNAseq", "GSM7720759", null, "source name:zebrafish larva|cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf loc name:missing|collection date:missing", "zebrafish larva  neurons and glia  scRNAseq", "using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish larva", null, "About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 \u00b0C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 \u03bcm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 \u00b0C for 25 min. The digestion was terminated by adding 500 \u03bcl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4\u00b0C  washed once with L15 and resuspended in 200 \u03bcl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 \u03bcm opening. The solution was filtered through a 35 \u03bcm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf", "GSM7720759", "GSM7720759: zebrafish larva  neurons and glia  scRNAseq; Danio rerio; RNA Seq", "GSM7720759 r1", "GSM7720759", "1", "About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 \u00b0C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 \u03bcm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 \u00b0C for 25 min. The digestion was terminated by adding 500 \u03bcl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4\u00b0C  washed once with L15 and resuspended in 200 \u03bcl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 \u03bcm opening. The solution was filtered through a 35 \u03bcm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP456253", null, "loader:fastq load.py", "CEL210928PB_HW1008_SAIG_D7_S1_L002_I1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L002_I2_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L002_R1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 55936355640.0, 254256162.0, "GSM7720759 r1", "0:10 1:10 2:100 3:100", "A:13207297968;C:10496996981;G:10989402500;T:16156355819;N:1179132", 10, 10, 100, 100, 13207297968, 10496996981, 10989402500, 16156355819, 1179132, "SRX21445937", "SRS18680715", "SRA1696793", "Oregon Health and Science Univ", "Oregon Health and Science Univ", 2, 0.0, 0.81961, 0.0, 0.19165, 1.0, 0.8508, null, 0.59575, 100, 100, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-21", "Larval", "Larval", "Multi-tissue", "Multi-system"], [25238, "SRR25721802", "SRX21445937", "SRS18680715", "SRP456253", "PRJNA1007646", "Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival [larva]", "GSE241296", "Other", "Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish  this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation  making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however  the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach  we demonstrate that larval RBs in zebrafish fall into three  largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities  including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover  this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib  which is used in clinic and causes peripheral neuropathy. Importantly  dovitinib mediated axon loss can be suppressed by loss of Sarm1  a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 \u00b0C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 \u00b5m respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 \u00b0C for 25 min. The digestion was terminated by adding 500 \u00b5l stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4\u00b0C  washed once with L15 and resuspended in 200 \u00b5l of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 \u00b5m opening. The solution was filtered through a 35 \u00b5m strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing", null, null, null, "zebrafish larva  neurons and glia  scRNAseq", "GSM7720759", null, "source name:zebrafish larva|cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf loc name:missing|collection date:missing", "zebrafish larva  neurons and glia  scRNAseq", "using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish larva", null, "About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 \u00b0C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 \u03bcm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 \u00b0C for 25 min. The digestion was terminated by adding 500 \u03bcl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4\u00b0C  washed once with L15 and resuspended in 200 \u03bcl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 \u03bcm opening. The solution was filtered through a 35 \u03bcm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf", "GSM7720759", "GSM7720759: zebrafish larva  neurons and glia  scRNAseq; Danio rerio; RNA Seq", "GSM7720759 r1", "GSM7720759", "1", "About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 \u00b0C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 \u03bcm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 \u00b0C for 25 min. The digestion was terminated by adding 500 \u03bcl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4\u00b0C  washed once with L15 and resuspended in 200 \u03bcl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 \u03bcm opening. The solution was filtered through a 35 \u03bcm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP456253", null, "loader:fastq load.py", "CEL210928PB_HW1008_SAIG_D7_S1_L001_I1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_I2_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_R1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 54474841080.0, 247612914.0, "GSM7720759 r2", "0:10 1:10 2:100 3:100", "A:12887048507;C:10210716068;G:10683375130;T:15740176261;N:1266834", 10, 10, 100, 100, 12887048507, 10210716068, 10683375130, 15740176261, 1266834, "SRX21445937", "SRS18680715", "SRA1696793", "Oregon Health and Science Univ", "Oregon Health and Science Univ", 2, 0.0, 0.82189, 0.0, 0.19349, 1.0, 0.85025, null, 0.6092, 100, 100, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-21", "Larval", "Larval", "Multi-tissue", "Multi-system"], [26482, "SRR25930974", "SRX21649989", "SRS18818461", "SRP458853", "PRJNA1013567", "scRNA seq of 50 hpf and 80 hpf isolated zebrafish hearts", "GSE242483", "Transcriptome Analysis", "Seeking to identify additional transcription factors required for cardiac valve formation  we determined and explored the transcriptional landscape of endocardial cells at the time when key morphogenetic events underlying valve development take place. Overall design: We isolated wild type zebrafish hearts at 50 hpf when valve identity has just been established  and at 80 hpf when forming valves are first observed", null, "pubmed:38748804", null, "80hpf", "GSM7764482", null, "source name:heart|tissue:heart|genotype:wild type|age:80hpf|geo loc name:missing|collection date:missing", "80hpf", "Reads were aligned against the zebrafish genome and counted by StarSolo. Preprocessed counts were further analysed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed cells that did not express more than 300 genes or had a mitochondrial content greater than 8%. Furthermore  we filtered genes if they were detected in less than 30 cells. Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA  retaining 50 principal components. Subsequent steps  like low dimensional UMAP embedding and cell clustering  were based on the initial PCA. Final data visualization was done by scanpy and cellxgene packages. Assembly: DanRer11 Supplementary files format and content: starsolo outputs", "heart", null, "Whole hearts were isolated and cardiac cells were dissociated. Dead cells were removed from the final cell isolate by FACs sorting in PBS without xxx and Magnesium and with 0.04% BSA. Each sample was run separately on a lane in a Chromium controller with Chromium Next GEM Single Cell 3\u02b9 Reagent Kits v3 1 10xGenomics.  scRNA seq library preparation was done using a standard protocol  and sequencing was done on a Nextseq2000", null, "tissue:heart|genotype:wild type|age:80hpf", "GSM7764482", "GSM7764482: 80hpf; Danio rerio; RNA Seq", "GSM7764482 r1", "GSM7764482", "1", "Whole hearts were isolated and cardiac cells were dissociated. Dead cells were removed from the final cell isolate by FACs sorting in PBS without xxx and Magnesium and with 0.04% BSA. Each sample was run separately on a lane in a Chromium controller with Chromium Next GEM Single Cell 3\u02b9 Reagent Kits v3 1 10xGenomics.  scRNA seq library preparation was done using a standard protocol  and sequencing was done on a Nextseq2000", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP458853", null, null, "Giulia_80hpf_S2_R1_001.fastq.gz Giulia_80hpf_S2_R2_001.fastq.gz", "fastq fastq", 18811433188.0, 225273324.0, "GSM7764482 r1", "0:28 1:55.50", "A:5135587480;C:4020079745;G:4129712330;T:5427444755;N:98608878", 28, 55, null, null, 5135587480, 4020079745, 4129712330, 5427444755, 98608878, "SRX21649989", "SRS18818461", "SRA1706674", "Bioinformatics, Max-Planck-Institute for Heart and Lung Research", "Bioinformatics, Max-Planck-Institute for Heart and Lung Research", 2, 0.00187, 0.93611, 0.00071, 0.16105, 0.99626, 0.79825, 0.41545, 0.50249, 28, 55, "T", "B", "sc-like readlen", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-09-06", "Larval", "Larval", "Heart", "Cardiovascular System"], [28771, "SRR26639098", "SRX22339478", "SRS19389127", "SRP469857", "PRJNA1034995", "Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.", "GSE246850", "Transcriptome Analysis", "Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.", null, "pubmed:39720516", null, "sibling  replicate 2  snRNAseq", "GSM7880035", null, "source name:heart|tissue:heart|age:3dpf|genotype:wt sibling|geo loc name:missing|collection date:missing", "sibling  replicate 2  snRNAseq", "The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix", "heart", null, "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3\u2019 gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "tissue:heart|age:3dpf|genotype:wt sibling", "GSM7880035", "GSM7880035: sibling  replicate 2  snRNAseq; Danio rerio; RNA Seq", "GSM7880035 r1", "GSM7880035", "1", "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469857", null, "loader:fastq load.py", "sib_2_S1_L001_R1_001.fastq.gz sib_2_S1_L001_R2_001.fastq.gz", "fastq fastq", 29585942468.0, 250728326.0, "GSM7880035 r1", "0:29 1:89", "A:8869085825;C:6519678188;G:6681924988;T:7515095066;N:158401", 29, 89, null, null, 8869085825, 6519678188, 6681924988, 7515095066, 158401, "SRX22339478", "SRS19389127", "SRA1744308", "University of Bern", "University of Bern", 2, 0.03708, 0.89742, 0.02638, 0.33817, 0.98766, 0.87265, 0.50529, 0.84547, 29, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2023-11-02", "Larval", "Larval", "Heart", "Cardiovascular System"], [28772, "SRR26639099", "SRX22339478", "SRS19389127", "SRP469857", "PRJNA1034995", "Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.", "GSE246850", "Transcriptome Analysis", "Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.", null, "pubmed:39720516", null, "sibling  replicate 2  snRNAseq", "GSM7880035", null, "source name:heart|tissue:heart|age:3dpf|genotype:wt sibling|geo loc name:missing|collection date:missing", "sibling  replicate 2  snRNAseq", "The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix", "heart", null, "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3\u2019 gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "tissue:heart|age:3dpf|genotype:wt sibling", "GSM7880035", "GSM7880035: sibling  replicate 2  snRNAseq; Danio rerio; RNA Seq", "GSM7880035 r1", "GSM7880035", "1", "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469857", null, "loader:fastq load.py", "sib_2_S1_L002_R1_001.fastq.gz sib_2_S1_L002_R2_001.fastq.gz", "fastq fastq", 29238445684.0, 247783438.0, "GSM7880035 r2", "0:29 1:89", "A:8764474921;C:6441070570;G:6601843083;T:7430828352;N:228758", 29, 89, null, null, 8764474921, 6441070570, 6601843083, 7430828352, 228758, "SRX22339478", "SRS19389127", "SRA1744308", "University of Bern", "University of Bern", 2, 0.03758, 0.89628, 0.02664, 0.33912, 0.98711, 0.87442, 0.4887, 0.42456, 29, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2023-11-02", "Larval", "Larval", "Heart", "Cardiovascular System"], [28773, "SRR26639100", "SRX22339477", "SRS19389126", "SRP469857", "PRJNA1034995", "Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.", "GSE246850", "Transcriptome Analysis", "Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.", null, "pubmed:39720516", null, "sibling  replicate 1  snRNAseq", "GSM7880034", null, "source name:heart|tissue:heart|age:3dpf|genotype:wt sibling|geo loc name:missing|collection date:missing", "sibling  replicate 1  snRNAseq", "The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix", "heart", null, "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3\u2019 gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "tissue:heart|age:3dpf|genotype:wt sibling", "GSM7880034", "GSM7880034: sibling  replicate 1  snRNAseq; Danio rerio; RNA Seq", "GSM7880034 r1", "GSM7880034", "1", "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469857", null, "loader:fastq load.py", "sib_1_S1_L001_R1_001.fastq.gz sib_1_S1_L001_R2_001.fastq.gz", "fastq fastq", 24652163520.0, 208916640.0, "GSM7880034 r1", "0:29 1:89", "A:7206225437;C:5487875216;G:5870141423;T:6087790451;N:130993", 29, 89, null, null, 7206225437, 5487875216, 5870141423, 6087790451, 130993, "SRX22339477", "SRS19389126", "SRA1744308", "University of Bern", "University of Bern", 2, 0.04136, 0.8662, 0.02868, 0.3899, 0.98597, 0.86906, 0.42284, 0.79265, 29, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2023-11-02", "Larval", "Larval", "Heart", "Cardiovascular System"], [28774, "SRR26639101", "SRX22339477", "SRS19389126", "SRP469857", "PRJNA1034995", "Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.", "GSE246850", "Transcriptome Analysis", "Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.", null, "pubmed:39720516", null, "sibling  replicate 1  snRNAseq", "GSM7880034", null, "source name:heart|tissue:heart|age:3dpf|genotype:wt sibling|geo loc name:missing|collection date:missing", "sibling  replicate 1  snRNAseq", "The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix", "heart", null, "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3\u2019 gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "tissue:heart|age:3dpf|genotype:wt sibling", "GSM7880034", "GSM7880034: sibling  replicate 1  snRNAseq; Danio rerio; RNA Seq", "GSM7880034 r1", "GSM7880034", "1", "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469857", null, "loader:fastq load.py", "sib_1_S1_L002_R1_001.fastq.gz sib_1_S1_L002_R2_001.fastq.gz", "fastq fastq", 24333156656.0, 206213192.0, "GSM7880034 r2", "0:29 1:89", "A:7112369699;C:5414867956;G:5792728480;T:6013000607;N:189914", 29, 89, null, null, 7112369699, 5414867956, 5792728480, 6013000607, 189914, "SRX22339477", "SRS19389126", "SRA1744308", "University of Bern", "University of Bern", 2, 0.04141, 0.86578, 0.02866, 0.39157, 0.98614, 0.8704, 0.42701, 0.78792, 29, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2023-11-02", "Larval", "Larval", "Heart", "Cardiovascular System"], [28775, "SRR26639102", "SRX22339476", "SRS19389125", "SRP469857", "PRJNA1034995", "Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.", "GSE246850", "Transcriptome Analysis", "Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.", null, "pubmed:39720516", null, "spns mutant  replicate 2  snRNAseq", "GSM7880033", null, "source name:heart|tissue:heart|age:3dpf|genotype:spns mutant|geo loc name:missing|collection date:missing", "spns mutant  replicate 2  snRNAseq", "The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix", "heart", null, "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3\u2019 gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "tissue:heart|age:3dpf|genotype:spns mutant", "GSM7880033", "GSM7880033: spns mutant  replicate 2  snRNAseq; Danio rerio; RNA Seq", "GSM7880033 r1", "GSM7880033", "1", "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469857", null, "loader:fastq load.py", "mut_2_S1_L001_R1_001.fastq.gz mut_2_S1_L001_R2_001.fastq.gz", "fastq fastq", 33067082062.0, 280229509.0, "GSM7880033 r1", "0:29 1:89", "A:9837791085;C:7302189072;G:7479072379;T:8447851569;N:177957", 29, 89, null, null, 9837791085, 7302189072, 7479072379, 8447851569, 177957, "SRX22339476", "SRS19389125", "SRA1744308", "University of Bern", "University of Bern", 2, 0.03975, 0.89392, 0.02827, 0.35098, 0.98693, 0.87572, 0.42665, 0.8308, 29, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2023-11-02", "Larval", "Larval", "Heart", "Cardiovascular System"], [28776, "SRR26639103", "SRX22339476", "SRS19389125", "SRP469857", "PRJNA1034995", "Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.", "GSE246850", "Transcriptome Analysis", "Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.", null, "pubmed:39720516", null, "spns mutant  replicate 2  snRNAseq", "GSM7880033", null, "source name:heart|tissue:heart|age:3dpf|genotype:spns mutant|geo loc name:missing|collection date:missing", "spns mutant  replicate 2  snRNAseq", "The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix", "heart", null, "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3\u2019 gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "tissue:heart|age:3dpf|genotype:spns mutant", "GSM7880033", "GSM7880033: spns mutant  replicate 2  snRNAseq; Danio rerio; RNA Seq", "GSM7880033 r1", "GSM7880033", "1", "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469857", null, "loader:fastq load.py", "mut_2_S1_L002_R1_001.fastq.gz mut_2_S1_L002_R2_001.fastq.gz", "fastq fastq", 32794778418.0, 277921851.0, "GSM7880033 r2", "0:29 1:89", "A:9757463504;C:7238976466;G:7415128557;T:8382951671;N:258220", 29, 89, null, null, 9757463504, 7238976466, 7415128557, 8382951671, 258220, "SRX22339476", "SRS19389125", "SRA1744308", "University of Bern", "University of Bern", 2, 0.04055, 0.89543, 0.02892, 0.35129, 0.98654, 0.87655, 0.45394, 0.85056, 29, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2023-11-02", "Larval", "Larval", "Heart", "Cardiovascular System"], [28777, "SRR26639104", "SRX22339475", "SRS19389124", "SRP469857", "PRJNA1034995", "Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.", "GSE246850", "Transcriptome Analysis", "Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.", null, "pubmed:39720516", null, "spns mutant  replicate 1  snRNAseq", "GSM7880032", null, "source name:heart|tissue:heart|age:3dpf|genotype:spns mutant|geo loc name:missing|collection date:missing", "spns mutant  replicate 1  snRNAseq", "The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix", "heart", null, "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3\u2019 gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "tissue:heart|age:3dpf|genotype:spns mutant", "GSM7880032", "GSM7880032: spns mutant  replicate 1  snRNAseq; Danio rerio; RNA Seq", "GSM7880032 r1", "GSM7880032", "1", "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469857", null, "loader:fastq load.py", "mut_1_S1_L001_R1_001.fastq.gz mut_1_S1_L001_R2_001.fastq.gz", "fastq fastq", 30027997254.0, 254474553.0, "GSM7880032 r1", "0:29 1:89", "A:9128230353;C:6473885422;G:6895366272;T:7530354635;N:160572", 29, 89, null, null, 9128230353, 6473885422, 6895366272, 7530354635, 160572, "SRX22339475", "SRS19389124", "SRA1744308", "University of Bern", "University of Bern", 2, 0.03908, 0.86231, 0.0274, 0.38263, 0.98701, 0.87113, 0.48114, 0.78783, 29, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2023-11-02", "Larval", "Larval", "Heart", "Cardiovascular System"], [28778, "SRR26639105", "SRX22339475", "SRS19389124", "SRP469857", "PRJNA1034995", "Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.", "GSE246850", "Transcriptome Analysis", "Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.", null, "pubmed:39720516", null, "spns mutant  replicate 1  snRNAseq", "GSM7880032", null, "source name:heart|tissue:heart|age:3dpf|genotype:spns mutant|geo loc name:missing|collection date:missing", "spns mutant  replicate 1  snRNAseq", "The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix", "heart", null, "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3\u2019 gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "tissue:heart|age:3dpf|genotype:spns mutant", "GSM7880032", "GSM7880032: spns mutant  replicate 1  snRNAseq; Danio rerio; RNA Seq", "GSM7880032 r1", "GSM7880032", "1", "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469857", null, "loader:fastq load.py", "mut_1_S1_L002_R1_001.fastq.gz mut_1_S1_L002_R2_001.fastq.gz", "fastq fastq", 29506651188.0, 250056366.0, "GSM7880032 r2", "0:29 1:89", "A:8967217701;C:6359649244;G:6775979696;T:7403576105;N:228442", 29, 89, null, null, 8967217701, 6359649244, 6775979696, 7403576105, 228442, "SRX22339475", "SRS19389124", "SRA1744308", "University of Bern", "University of Bern", 2, 0.03885, 0.86188, 0.02749, 0.38666, 0.98644, 0.86975, 0.46306, 0.79451, 29, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2023-11-02", "Larval", "Larval", "Heart", "Cardiovascular System"], [29174, "SRR27237224", "SRX22915658", "SRS19883761", "SRP478464", "PRJNA1053781", "Single cell gene expression profie of developing photoreceptor cells in larval zebrafish", "GSE250379", "Other", "Molecular underpinnings of vertebrate retinal differentiation and maturation are poorly understood  particularly for non mammalian species. We generated single cell transcriptome data from the larval zebrafish retina and characterized gene expression diversity among photoreceptor subtypes and their progenitors. Overall design: GFP positive differentiating photoreceptor cells and bipolar cells were collected from 4 dpf larval transgenic zebrafish  Tgcrx:EGFPstl887  using fluorescence activated cell sorting.", "parent bioproject:PRJNA1050288", "pubmed:39531499", null, "retina  scRNA seq", "GSM7978132", null, "source name:retina|tissue:retina|genotype:Tgcrx:EGFPstl887|developmental stage:4 dpf|geo loc name:missing|collection date:missing", "retina  scRNA seq", "Read alignment and initial quality control were performed using Cell Ranger software version 7.0.0  10X Genomics. Assembly: GRCz11 Supplementary files format and content: Tab separated value file and matrix file", "retina", null, "Fifty heads were dissected from 4 dpf heterozygous Tgcrx:GFPstl887Tg larvae. Following dissection  eyes were stored in ice cold Hanks\u2019 Balanced Salt Solution HBSS until all eyes were harvested. Once the eyes were collected  HBSS was removed and the eyes were incubated in 400 \u00b5l of calcium/magnesium free HBSS containing 0.4 mg papain Worthington Biochem for 15 min at 37\u00b0C. 800 \u00b5l of 10% fetal bovine serum FBS in Dulbecco's Modified Eagle Medium DMEM containing 5mM MgCl2 and 120 units DNaseI Roche were added to the mixture and incubated for 5 min at 37\u00b0C. Cells were then resuspended in 300 \u00b5l of sorting buffer 2.5 mM EDTA  25 mM HEPES  1% bovine serum albumin BSA in calcium/magnesium free HBSS. Cells were sorted on an Aria II FACS machine BD biosciences with gating based on forward scatter  side scatter  and GFP fluorescence and collected in 700 \u03bcl of D PBS without xxx+ and Mg2+  supplemented with 0.4 % BSA D PBS CMF in 1.5 ml microcentrifuge tubes. The collected cells were then centrifuged at 300\u00d7g for 5 min  washed with D PBS CMF  centrifuged  and supernatant reduced to 80 \u00b5l. Cell density was quantified on a hemocytometer  and  5000 cells were used for single cell library preparation. A library for single cell RNA seq was constructed with the Chromium v3  platform  10X  Genomics   Pleasanton   CA according to the manufacturer protocol.", null, "tissue:retina|genotype:Tgcrx:EGFPstl887|developmental stage:4 dpf", "GSM7978132", "GSM7978132: retina  scRNA seq; Danio rerio; RNA Seq", "GSM7978132 r1", "GSM7978132", "1", "Fifty heads were dissected from 4 dpf heterozygous Tgcrx:GFPstl887Tg larvae. Following dissection  eyes were stored in ice cold Hanks' Balanced Salt Solution HBSS until all eyes were harvested. Once the eyes were collected  HBSS was removed and the eyes were incubated in 400 \u00b5l of calcium/magnesium free HBSS containing 0.4 mg papain Worthington Biochem for 15 min at 37\u00b0C. 800 \u00b5l of 10% fetal bovine serum FBS in Dulbecco's Modified Eagle Medium DMEM containing 5mM MgCl2 and 120 units DNaseI Roche were added to the mixture and incubated for 5 min at 37\u00b0C. Cells were then resuspended in 300 \u00b5l of sorting buffer 2.5 mM EDTA  25 mM HEPES  1% bovine serum albumin BSA in calcium/magnesium free HBSS. Cells were sorted on an Aria II FACS machine BD biosciences with gating based on forward scatter  side scatter  and GFP fluorescence and collected in 700 \u03bcl of D PBS without xxx+ and Mg2+  supplemented with 0.4 % BSA D PBS CMF in 1.5 ml microcentrifuge tubes. The collected cells were then centrifuged at 300\u00d7g for 5 min  washed with D PBS CMF  centrifuged  and supernatant reduced to 80 \u00b5l. Cell density was quantified on a hemocytometer  and  5000 cells were used for single cell library preparation. A library for single cell RNA seq was constructed with the Chromium v3  platform  10X  Genomics   Pleasanton   CA according to the manufacturer protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP478464", null, "loader:fastq load.py", "crx.crx_S1_L003_R1_001.fastq.gz crx.crx_S1_L003_R2_001.fastq.gz", "fastq fastq", 45170138494.0, 253764823.0, "GSM7978132 r1", "0:28 1:150", "A:13826023801;C:9023674621;G:9590649474;T:12728940802;N:849796", 28, 150, null, null, 13826023801, 9023674621, 9590649474, 12728940802, 849796, "SRX22915658", "SRS19883761", "SRA1770358", "Pathology and Immunology, Washington University School of Medicine", "Pathology and Immunology, Washington University School of Medicine", 2, 0.0046, 0.87155, 0.00206, 0.2263, 0.99168, 0.77784, 0.30223, 0.50112, 28, 150, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-12-17", "Larval", "Larval", "Eye", "Sensory System"], [29187, "SRR8176747", "SRX4996876", "SRS4031879", "SRP480945", "PRJNA1055160", "Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain", "PRJNA1055160", "Other", "We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf", null, "pubmed:38529407", null, "Nadia 19dpf ZZ Gonad Single Cell RNA Seq", "Nadia 19dpf ZZ Gonad Single Cell RNA Seq", null, "strain:Nadia|age:19 dpf provider:John H. Postlethwait  University of Oregon|genotype:ZZ|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA Seq of Danio rerio: Nadia 19dpf ZZ gonad", "Nadia 19dpf ZZ gonad", "Nadia 19dpf ZZ gonad", "A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP480945", null, "loader:fastq load.py", null, null, 15090036999.0, 107021539.0, "zz 19NAmale I1 001.fastq.gz", "0:8 1:133", "A:4154103253;C:3402890354;G:3765557416;T:3755723849;N:11762127", 8, 133, null, null, 4154103253, 3402890354, 3765557416, 3755723849, 11762127, "SRX4996876", "SRS4031879", "SRA807619", "University of Oregon|Institute of Neuroscience", "University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2018-11-08", "Larval", "Larval", "Gonad", "Reproductive System"], [29190, "SRR8176756", "SRX4996867", "SRS4031876", "SRP480945", "PRJNA1055160", "Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain", "PRJNA1055160", "Other", "We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf", null, "pubmed:38529407", null, "Nadia 19dpf ZW Gonad Single Cell RNA Seq", "Nadia 19dpf ZW Gonad Single Cell RNA Seq", null, "strain:Nadia|age:19 dpf provider:John H. Postlethwait  University of Oregon|genotype:ZW|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA Seq of Danio rerio: Nadia 19dpf ZW gonad", "Nadia 19dpf ZW gonad", "Nadia 19dpf ZW gonad", "A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP480945", null, "loader:fastq load.py", null, null, 17141425554.0, 121570394.0, "zw 19NAfem I1 001.fastq.gz", "0:8 1:133", "A:4656207219;C:3824531650;G:4322736498;T:4324676442;N:13273745", 8, 133, null, null, 4656207219, 3824531650, 4322736498, 4324676442, 13273745, "SRX4996867", "SRS4031876", "SRA807619", "University of Oregon|Institute of Neuroscience", "University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2018-11-08", "Larval", "Larval", "Gonad", "Reproductive System"], [30692, "SRR29655998", "SRX25159999", "SRS21850513", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC145382 HuNoV infected  replicate 1  scRNAseq", "GSM8370069", null, "tissue:Tg mpeg:mCherry|cell line:Tg mpeg:mCherry|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing", "GC145382 HuNoV infected  replicate 1  scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: hg38 Supplementary files format and content: Count Matrix Cell Ranger", "Tg mpeg:mCherry", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "cell line:Tg mpeg:mCherry|cell type:120 hpf|infection:HuNoV infected", "GSM8370069", "GSM8370069: GC145382 HuNoV infected  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM8370069 r1", "GSM8370069", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC145382_SI-GA-B1_S1_L001_R1_001.fastq.gz GC145382_SI-GA-B1_S1_L001_R2_001.fastq.gz", "fastq fastq", 5781664526.0, 48997157.0, "GSM8370069 r1", "0:28 1:90", "A:1659071356;C:1268706433;G:1342749232;T:1510681009;N:456496", 28, 90, null, null, 1659071356, 1268706433, 1342749232, 1510681009, 456496, "SRX25159999", "SRS21850513", "SRA1913292", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-06-30", "Larval", "Larval", "Cell Line", "Cell Line"], [30693, "SRR29655999", "SRX25159999", "SRS21850513", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC145382 HuNoV infected  replicate 1  scRNAseq", "GSM8370069", null, "tissue:Tg mpeg:mCherry|cell line:Tg mpeg:mCherry|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing", "GC145382 HuNoV infected  replicate 1  scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: hg38 Supplementary files format and content: Count Matrix Cell Ranger", "Tg mpeg:mCherry", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "cell line:Tg mpeg:mCherry|cell type:120 hpf|infection:HuNoV infected", "GSM8370069", "GSM8370069: GC145382 HuNoV infected  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM8370069 r1", "GSM8370069", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC145382_SI-GA-B1_S1_L002_R1_001.fastq.gz GC145382_SI-GA-B1_S1_L002_R2_001.fastq.gz", "fastq fastq", 6046508328.0, 51241596.0, "GSM8370069 r2", "0:28 1:90", "A:1731027394;C:1330440539;G:1408717533;T:1575870623;N:452239", 28, 90, null, null, 1731027394, 1330440539, 1408717533, 1575870623, 452239, "SRX25159999", "SRS21850513", "SRA1913292", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-06-30", "Larval", "Larval", "Cell Line", "Cell Line"], [30694, "SRR28272066", "SRX23882001", "SRS20705714", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC122775  HuNoV infected  replicate 2 scRNAseq", "GSM8136771", null, "source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing", "GC122775  HuNoV infected  replicate 2 scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger", "Intestines", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected", "GSM8136771", "GSM8136771: GC122775  HuNoV infected  replicate 2 scRNAseq; Danio rerio; RNA Seq", "GSM8136771 r1", "GSM8136771", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC122775_SI-GA-D7_S4_L001_R1_001.fastq.gz GC122775_SI-GA-D7_S4_L001_R2_001.fastq.gz", "fastq fastq", 6487168261.0, 54514019.0, "GSM8136771 r1", "0:28 1:91", "A:1754199332;C:1533792234;G:1687916105;T:1511168304;N:92286", 28, 91, null, null, 1754199332, 1533792234, 1687916105, 1511168304, 92286, "SRX23882001", "SRS20705714", "SRA1820104", "Genomics Core Leuven", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-03-08", "Larval", "Larval", "Gut", "Digestive System"], [30695, "SRR28272067", "SRX23882001", "SRS20705714", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC122775  HuNoV infected  replicate 2 scRNAseq", "GSM8136771", null, "source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing", "GC122775  HuNoV infected  replicate 2 scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger", "Intestines", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected", "GSM8136771", "GSM8136771: GC122775  HuNoV infected  replicate 2 scRNAseq; Danio rerio; RNA Seq", "GSM8136771 r1", "GSM8136771", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC122775_SI-GA-D7_S4_L002_R1_001.fastq.gz GC122775_SI-GA-D7_S4_L002_R2_001.fastq.gz", "fastq fastq", 6313572727.0, 53055233.0, "GSM8136771 r2", "0:28 1:91", "A:1709609257;C:1491468410;G:1640296277;T:1472111501;N:87282", 28, 91, null, null, 1709609257, 1491468410, 1640296277, 1472111501, 87282, "SRX23882001", "SRS20705714", "SRA1820104", "Genomics Core Leuven", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-03-08", "Larval", "Larval", "Gut", "Digestive System"], [30696, "SRR28272068", "SRX23882000", "SRS20705713", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC122774  HuNoV infected  replicate 1  scRNAseq", "GSM8136770", null, "source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing", "GC122774  HuNoV infected  replicate 1  scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger", "Intestines", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected", "GSM8136770", "GSM8136770: GC122774  HuNoV infected  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM8136770 r1", "GSM8136770", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC122774_SI-GA-C7_S3_L001_R1_001.fastq.gz GC122774_SI-GA-C7_S3_L001_R2_001.fastq.gz", "fastq fastq", 15738518978.0, 132256462.0, "GSM8136770 r1", "0:28 1:91", "A:4181691582;C:3761213961;G:4083789142;T:3711597081;N:227212", 28, 91, null, null, 4181691582, 3761213961, 4083789142, 3711597081, 227212, "SRX23882000", "SRS20705713", "SRA1820104", "Genomics Core Leuven", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-03-08", "Larval", "Larval", "Gut", "Digestive System"], [30697, "SRR28272069", "SRX23882000", "SRS20705713", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC122774  HuNoV infected  replicate 1  scRNAseq", "GSM8136770", null, "source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing", "GC122774  HuNoV infected  replicate 1  scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger", "Intestines", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected", "GSM8136770", "GSM8136770: GC122774  HuNoV infected  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM8136770 r1", "GSM8136770", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC122774_SI-GA-C7_S3_L002_R1_001.fastq.gz GC122774_SI-GA-C7_S3_L002_R2_001.fastq.gz", "fastq fastq", 15261653253.0, 128249187.0, "GSM8136770 r2", "0:28 1:91", "A:4059552936;C:3644406570;G:3954261902;T:3603216152;N:215693", 28, 91, null, null, 4059552936, 3644406570, 3954261902, 3603216152, 215693, "SRX23882000", "SRS20705713", "SRA1820104", "Genomics Core Leuven", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-03-08", "Larval", "Larval", "Gut", "Digestive System"], [30698, "SRR28272070", "SRX23881999", "SRS20705712", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC122773  uninfected  replicate 2  scRNAseq", "GSM8136769", null, "source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing", "GC122773  uninfected  replicate 2  scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger", "Intestines", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected", "GSM8136769", "GSM8136769: GC122773  uninfected  replicate 2  scRNAseq; Danio rerio; RNA Seq", "GSM8136769 r1", "GSM8136769", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC122773_SI-GA-B7_S2_L001_R1_001.fastq.gz GC122773_SI-GA-B7_S2_L001_R2_001.fastq.gz", "fastq fastq", 15150656598.0, 127316442.0, "GSM8136769 r1", "0:28 1:91", "A:4100783574;C:3526779401;G:3845684506;T:3677189004;N:220113", 28, 91, null, null, 4100783574, 3526779401, 3845684506, 3677189004, 220113, "SRX23881999", "SRS20705712", "SRA1820104", "Genomics Core Leuven", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-03-08", "Larval", "Larval", "Gut", "Digestive System"], [30699, "SRR28272071", "SRX23881999", "SRS20705712", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC122773  uninfected  replicate 2  scRNAseq", "GSM8136769", null, "source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing", "GC122773  uninfected  replicate 2  scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger", "Intestines", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected", "GSM8136769", "GSM8136769: GC122773  uninfected  replicate 2  scRNAseq; Danio rerio; RNA Seq", "GSM8136769 r1", "GSM8136769", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC122773_SI-GA-B7_S2_L002_R1_001.fastq.gz GC122773_SI-GA-B7_S2_L002_R2_001.fastq.gz", "fastq fastq", 14942015326.0, 125563154.0, "GSM8136769 r2", "0:28 1:91", "A:4048600218;C:3475105088;G:3787275869;T:3630822343;N:211808", 28, 91, null, null, 4048600218, 3475105088, 3787275869, 3630822343, 211808, "SRX23881999", "SRS20705712", "SRA1820104", "Genomics Core Leuven", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-03-08", "Larval", "Larval", "Gut", "Digestive System"], [30700, "SRR28272072", "SRX23881998", "SRS20705711", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC122772  uninfected  replicate 1  scRNAseq", "GSM8136768", null, "source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing", "GC122772  uninfected  replicate 1  scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger", "Intestines", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected", "GSM8136768", "GSM8136768: GC122772  uninfected  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM8136768 r1", "GSM8136768", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC122772_SI-GA-A7_S1_L001_R1_001.fastq.gz GC122772_SI-GA-A7_S1_L001_R2_001.fastq.gz", "fastq fastq", 7397061301.0, 62160179.0, "GSM8136768 r1", "0:28 1:91", "A:2023651844;C:1711760729;G:1860691426;T:1800850496;N:106806", 28, 91, null, null, 2023651844, 1711760729, 1860691426, 1800850496, 106806, "SRX23881998", "SRS20705711", "SRA1820104", "Genomics Core Leuven", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-03-08", "Larval", "Larval", "Gut", "Digestive System"], [30701, "SRR28272073", "SRX23881998", "SRS20705711", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC122772  uninfected  replicate 1  scRNAseq", "GSM8136768", null, "source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing", "GC122772  uninfected  replicate 1  scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger", "Intestines", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected", "GSM8136768", "GSM8136768: GC122772  uninfected  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM8136768 r1", "GSM8136768", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC122772_SI-GA-A7_S1_L002_R1_001.fastq.gz GC122772_SI-GA-A7_S1_L002_R2_001.fastq.gz", "fastq fastq", 7290496444.0, 61264676.0, "GSM8136768 r2", "0:28 1:91", "A:1996736343;C:1685693360;G:1830823892;T:1777138653;N:104196", 28, 91, null, null, 1996736343, 1685693360, 1830823892, 1777138653, 104196, "SRX23881998", "SRS20705711", "SRA1820104", "Genomics Core Leuven", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-03-08", "Larval", "Larval", "Gut", "Digestive System"], [30775, "SRR28357669", "SRX23962905", "SRS20762620", "SRP495490", "PRJNA1088483", "Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression [scRNA Seq]", "GSE261718", "Other", "Purpose: To explore the endogenous expression pattern of Erbb2. Methods:  Approximately 1000 hearts dissected from 72 hpf Tgmyl7:mCherry embryos were digested in 0.25% trypsin EDTA solution for single cell RNA sequencing. Results: We found that ventricular Erbb2 expression was highly enriched in subcluster 0 and 2  but weakly expressed in subcluster 3  10 and 12. Conclusions: Erbb2 exhibits heterogeneous expression during trabeculation. Overall design: 72 hpf Tgmyl7:mCherry zebrafish hearts were collected for single cell RNA sequencing.", null, "pubmed:40053597", null, "S72hpf trunks", "GSM8149579", null, "source name:zebrafish hearts|tissue:zebrafish hearts|cell line:Tgmyl7:mCherry heart cells|cell type:zebrafish heart cells|geo loc name:missing|collection date:missing", "S72hpf trunks", "Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 Supplementary files format and content: zip compressed  files include filtered gene bc matrices post running CellRanger pipeline", "zebrafish hearts", null, "A total of 1000 hearts dissected from Tgmyl7:mCherry embryos at 72 hpf were digested in 0.25% trypsin EDTA solution at 37 \u00b0C for 30 min. Single cell RNA seq library construction was performed using a droplet based library prep platform Chromium 10x Genomics with a Chromium Single Cell Reagent Kit according to the manufacturer\u2019s instructions. Single cell RNA Seq 10x", "Dechorionated zebrafish embryos were maintained in 0.3x Danieau\u2019s Buffer at 28 \u00b0C with a photoperiod of 14/10\u2009h light/dark.", "tissue:zebrafish hearts|cell line:Tgmyl7:mCherry heart cells|cell type:zebrafish heart cells", "GSM8149579", "GSM8149579: S72hpf trunks; Danio rerio; RNA Seq", "GSM8149579 r1", "GSM8149579", "1", "A total of 1000 hearts dissected from Tgmyl7:mCherry embryos at 72 hpf were digested in 0.25% trypsin EDTA solution at 37 \u00b0C for 30 min. Single cell RNA seq library construction was performed using a droplet based library prep platform Chromium 10x Genomics with a Chromium Single Cell Reagent Kit according to the manufacturer's instructions. Single cell RNA Seq 10x", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495490", null, null, "zebrafish_heart_72h_R1_fastq.gz zebrafish_heart_72h_R2_fastq.gz", "fastq fastq", 155978889600.0, 519929632.0, "GSM8149579 r1", "0:150 1:150", "A:63302225780;C:28042347630;G:26792086978;T:37838422350;N:3806862", 150, 150, null, null, 63302225780, 28042347630, 26792086978, 37838422350, 3806862, "SRX23962905", "SRS20762620", "SRA1825277", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.0, 0.92044, 0.0, 0.11022, 1.0, 0.80996, null, 0.54499, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-03-15", "Larval", "Larval", "Heart", "Cardiovascular System"], [31525, "SRR28419473", "SRX24023800", "SRS20818155", "SRP497235", "PRJNA1090867", "Single cell RNA seq of zebrafish endothelial cells", "GSE262232", "Transcriptome Analysis", "We performed single cell RNA sequencing scRNA seq for isolated endothelial cells Overall design: Tgkdrl:EGFP zebrafish embryos were digested into single cell suspension  EGFP positive cells were isolated using FACS and subjected to 10X Genomics Chromium scRNAseq.", null, "pubmed:39977018", null, "Zebrafish endothelial cells 3 dpf 2", "GSM8160887", null, "source name:Whole body|tissue:Whole body|age:embryo|geo loc name:missing|collection date:missing", "Zebrafish endothelial cells 3 dpf 2", "Cell Ranger v2.1 was used to de multiplex raw base call BCL files generated by Illumina sequencers into FASTQ files  perform the alignment  barcode counting  and UMI counting. Assembly: GRCz11 Supplementary files format and content: Tab seprated values files", "Whole body", null, "Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions  EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3\u2032 GEM  Library and Gel Bead Kit v2 10X Genomics according to manufacturer\u2019s protocol.", null, "tissue:Whole body|age:embryo", "GSM8160887", "GSM8160887: Zebrafish endothelial cells 3 dpf 2; Danio rerio; RNA Seq", "GSM8160887 r1", "GSM8160887", "1", "Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions  EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3\u2032 GEM  Library and Gel Bead Kit v2 10X Genomics according to manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP497235", null, "assembly:GRCz11|intentional duplicate|dangling references:treat as unmapped|dangling references:skip reference resolution", "3dpf_2_possorted_genome_bam.bam", "10X Genomics bam file", 8478190406.0, 86512147.0, "GSM8160887 r1", "0:98", "A:2448546566;C:1819820402;G:2005413327;T:2187171703;N:17238408", 98, null, null, null, 2448546566, 1819820402, 2005413327, 2187171703, 17238408, "SRX24023800", "SRS20818155", "SRA1835509", "Uppsala University", "Uppsala University", 1, 0.91631, null, 0.11199, null, 0.82106, null, 0.54746, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Sweden", "2024-03-22", "Larval", "Larval", "Trunk", "Surface Structure"], [31526, "SRR28419474", "SRX24023799", "SRS20818156", "SRP497235", "PRJNA1090867", "Single cell RNA seq of zebrafish endothelial cells", "GSE262232", "Transcriptome Analysis", "We performed single cell RNA sequencing scRNA seq for isolated endothelial cells Overall design: Tgkdrl:EGFP zebrafish embryos were digested into single cell suspension  EGFP positive cells were isolated using FACS and subjected to 10X Genomics Chromium scRNAseq.", null, "pubmed:39977018", null, "Zebrafish endothelial cells 3 dpf 1", "GSM8160886", null, "source name:Whole body|tissue:Whole body|age:embryo|geo loc name:missing|collection date:missing", "Zebrafish endothelial cells 3 dpf 1", "Cell Ranger v2.1 was used to de multiplex raw base call BCL files generated by Illumina sequencers into FASTQ files  perform the alignment  barcode counting  and UMI counting. Assembly: GRCz11 Supplementary files format and content: Tab seprated values files", "Whole body", null, "Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions  EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3\u2032 GEM  Library and Gel Bead Kit v2 10X Genomics according to manufacturer\u2019s protocol.", null, "tissue:Whole body|age:embryo", "GSM8160886", "GSM8160886: Zebrafish endothelial cells 3 dpf 1; Danio rerio; RNA Seq", "GSM8160886 r1", "GSM8160886", "1", "Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions  EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3\u2032 GEM  Library and Gel Bead Kit v2 10X Genomics according to manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP497235", null, "assembly:GRCz11|intentional duplicate|dangling references:treat as unmapped|dangling references:skip reference resolution", "3dpf_1_possorted_genome_bam.bam", "10X Genomics bam file", 2842123088.0, 29001256.0, "GSM8160886 r1", "0:98", "A:821846800;C:603425858;G:657525459;T:720690292;N:38634679", 98, null, null, null, 821846800, 603425858, 657525459, 720690292, 38634679, "SRX24023799", "SRS20818156", "SRA1835509", "Uppsala University", "Uppsala University", 1, 0.86292, null, 0.0954, null, 0.82844, null, 0.52761, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Sweden", "2024-03-22", "Larval", "Larval", "Trunk", "Surface Structure"], [31855, "SRR28735563", "SRX24301542", "SRS21065461", "SRP502616", "PRJNA1101946", "Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]", "GSE264310", "Transcriptome Analysis", "Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests  staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum  and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL   ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer  which includes amacrine cells among others  showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b /  ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates   30 larvae per each sample and Tg control  2 replicates  30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.", "parent bioproject:PRJNA1101942", "pubmed:39424970", null, "stim2KO  repllicate 2  scRNASeq", "GSM8215882", null, "source name:head|tissue:head|cell type:neuronal|genotype:stim2a;stim2b /  ; TgHuC:GCaMP5G|age:5 dpf larvae|geo loc name:missing|collection date:missing", "stim2KO  repllicate 2  scRNASeq", "Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR  for each sample with the following parameters:   soloType CB UMI Simple    soloCBwhitelist 3M february 2018.txt [from Cell Ranger]    soloUMIlen 12    soloCBmatchWLtype 1MM multi Nbase pseudocounts    soloUMIfiltering MultiGeneUMI CR    soloUMIdedup 1MM CR    soloCellFilter  EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "head", null, "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco\u2019s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit\u2019s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer\u2019s protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual\u2019s guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "tissue:head|cell type:neuronal|genotype:stim2a;stim2b /  ; TgHuC:GCaMP5G|age:5 dpf larvae", "GSM8215882", "GSM8215882: stim2KO  repllicate 2  scRNASeq; Danio rerio; RNA Seq", "GSM8215882 r1", "GSM8215882", "1", "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer's protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP502616", null, null, "RIS_F63_0006_P24_V11_S5_R2_001.fastq.gz RIS_F63_0006_P24_V11_S5_R1_001.fastq.gz", "fastq fastq", 18259545984.0, 142652703.0, "GSM8215882 r1", "0:28 1:100", "A:5244714575;C:3875508560;G:4200332154;T:4938304565;N:686130", 28, 100, null, null, 5244714575, 3875508560, 4200332154, 4938304565, 686130, "SRX24301542", "SRS21065461", "SRA1848620", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", 2, 0.0154, 0.87839, 0.00603, 0.34485, 0.99011, 0.78403, 0.22547, 0.56166, 28, 100, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Poland", "2024-04-18", "Larval", "Larval", "Head", "Nervous System"], [31856, "SRR28735564", "SRX24301542", "SRS21065461", "SRP502616", "PRJNA1101946", "Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]", "GSE264310", "Transcriptome Analysis", "Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests  staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum  and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL   ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer  which includes amacrine cells among others  showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b /  ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates   30 larvae per each sample and Tg control  2 replicates  30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.", "parent bioproject:PRJNA1101942", "pubmed:39424970", null, "stim2KO  repllicate 2  scRNASeq", "GSM8215882", null, "source name:head|tissue:head|cell type:neuronal|genotype:stim2a;stim2b /  ; TgHuC:GCaMP5G|age:5 dpf larvae|geo loc name:missing|collection date:missing", "stim2KO  repllicate 2  scRNASeq", "Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR  for each sample with the following parameters:   soloType CB UMI Simple    soloCBwhitelist 3M february 2018.txt [from Cell Ranger]    soloUMIlen 12    soloCBmatchWLtype 1MM multi Nbase pseudocounts    soloUMIfiltering MultiGeneUMI CR    soloUMIdedup 1MM CR    soloCellFilter  EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "head", null, "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco\u2019s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit\u2019s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer\u2019s protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual\u2019s guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "tissue:head|cell type:neuronal|genotype:stim2a;stim2b /  ; TgHuC:GCaMP5G|age:5 dpf larvae", "GSM8215882", "GSM8215882: stim2KO  repllicate 2  scRNASeq; Danio rerio; RNA Seq", "GSM8215882 r1", "GSM8215882", "1", "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer's protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP502616", null, null, "RIS_F63_0006_P24_V12_S6_R2_001.fastq.gz RIS_F63_0006_P24_V12_S6_R1_001.fastq.gz", "fastq fastq", 17876561664.0, 139660638.0, "GSM8215882 r2", "0:28 1:100", "A:5103195386;C:3808218494;G:4122439805;T:4842033472;N:674507", 28, 100, null, null, 5103195386, 3808218494, 4122439805, 4842033472, 674507, "SRX24301542", "SRS21065461", "SRA1848620", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", 2, 0.01605, 0.88209, 0.00613, 0.34048, 0.99005, 0.78569, 0.24462, 0.56679, 28, 100, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Poland", "2024-04-18", "Larval", "Larval", "Head", "Nervous System"], [31857, "SRR28735565", "SRX24301542", "SRS21065461", "SRP502616", "PRJNA1101946", "Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]", "GSE264310", "Transcriptome Analysis", "Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests  staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum  and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL   ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer  which includes amacrine cells among others  showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b /  ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates   30 larvae per each sample and Tg control  2 replicates  30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.", "parent bioproject:PRJNA1101942", "pubmed:39424970", null, "stim2KO  repllicate 2  scRNASeq", "GSM8215882", null, "source name:head|tissue:head|cell type:neuronal|genotype:stim2a;stim2b /  ; TgHuC:GCaMP5G|age:5 dpf larvae|geo loc name:missing|collection date:missing", "stim2KO  repllicate 2  scRNASeq", "Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR  for each sample with the following parameters:   soloType CB UMI Simple    soloCBwhitelist 3M february 2018.txt [from Cell Ranger]    soloUMIlen 12    soloCBmatchWLtype 1MM multi Nbase pseudocounts    soloUMIfiltering MultiGeneUMI CR    soloUMIdedup 1MM CR    soloCellFilter  EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "head", null, "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco\u2019s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit\u2019s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer\u2019s protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual\u2019s guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "tissue:head|cell type:neuronal|genotype:stim2a;stim2b /  ; TgHuC:GCaMP5G|age:5 dpf larvae", "GSM8215882", "GSM8215882: stim2KO  repllicate 2  scRNASeq; Danio rerio; RNA Seq", "GSM8215882 r1", "GSM8215882", "1", "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer's protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP502616", null, null, "RIS_F63_0006_P24_V13_S7_R2_001.fastq.gz RIS_F63_0006_P24_V13_S7_R1_001.fastq.gz", "fastq fastq", 11789486464.0, 92105363.0, "GSM8215882 r3", "0:28 1:100", "A:3373601519;C:2511268571;G:2715549864;T:3188625976;N:440534", 28, 100, null, null, 3373601519, 2511268571, 2715549864, 3188625976, 440534, "SRX24301542", "SRS21065461", "SRA1848620", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", 2, 0.01608, 0.87817, 0.00612, 0.34136, 0.98979, 0.78626, 0.23961, 0.56904, 28, 100, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Poland", "2024-04-18", "Larval", "Larval", "Head", "Nervous System"], [31858, "SRR28735566", "SRX24301542", "SRS21065461", "SRP502616", "PRJNA1101946", "Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]", "GSE264310", "Transcriptome Analysis", "Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests  staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum  and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL   ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer  which includes amacrine cells among others  showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b /  ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates   30 larvae per each sample and Tg control  2 replicates  30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.", "parent bioproject:PRJNA1101942", "pubmed:39424970", null, "stim2KO  repllicate 2  scRNASeq", "GSM8215882", null, "source name:head|tissue:head|cell type:neuronal|genotype:stim2a;stim2b /  ; TgHuC:GCaMP5G|age:5 dpf larvae|geo loc name:missing|collection date:missing", "stim2KO  repllicate 2  scRNASeq", "Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR  for each sample with the following parameters:   soloType CB UMI Simple    soloCBwhitelist 3M february 2018.txt [from Cell Ranger]    soloUMIlen 12    soloCBmatchWLtype 1MM multi Nbase pseudocounts    soloUMIfiltering MultiGeneUMI CR    soloUMIdedup 1MM CR    soloCellFilter  EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "head", null, "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco\u2019s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit\u2019s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer\u2019s protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual\u2019s guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "tissue:head|cell type:neuronal|genotype:stim2a;stim2b /  ; TgHuC:GCaMP5G|age:5 dpf larvae", "GSM8215882", "GSM8215882: stim2KO  repllicate 2  scRNASeq; Danio rerio; RNA Seq", "GSM8215882 r1", "GSM8215882", "1", "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer's protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP502616", null, null, "RIS_F63_0006_P24_V14_S8_R2_001.fastq.gz RIS_F63_0006_P24_V14_S8_R1_001.fastq.gz", "fastq fastq", 15492682752.0, 121036584.0, "GSM8215882 r4", "0:28 1:100", "A:4403489633;C:3300131260;G:3589771700;T:4198706550;N:583609", 28, 100, null, null, 4403489633, 3300131260, 3589771700, 4198706550, 583609, "SRX24301542", "SRS21065461", "SRA1848620", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", 2, 0.0161, 0.88184, 0.0062, 0.34153, 0.99072, 0.78593, 0.23108, 0.5637, 28, 100, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Poland", "2024-04-18", "Larval", "Larval", "Head", "Nervous System"], [31859, "SRR28735567", "SRX24301541", "SRS21065460", "SRP502616", "PRJNA1101946", "Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]", "GSE264310", "Transcriptome Analysis", "Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests  staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum  and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL   ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer  which includes amacrine cells among others  showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b /  ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates   30 larvae per each sample and Tg control  2 replicates  30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.", "parent bioproject:PRJNA1101942", "pubmed:39424970", null, "stim2KO  repllicate 1  scRNASeq", "GSM8215881", null, "source name:head|tissue:head|cell type:neuronal|genotype:stim2a;stim2b /  ; TgHuC:GCaMP5G|age:5 dpf larvae|geo loc name:missing|collection date:missing", "stim2KO  repllicate 1  scRNASeq", "Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR  for each sample with the following parameters:   soloType CB UMI Simple    soloCBwhitelist 3M february 2018.txt [from Cell Ranger]    soloUMIlen 12    soloCBmatchWLtype 1MM multi Nbase pseudocounts    soloUMIfiltering MultiGeneUMI CR    soloUMIdedup 1MM CR    soloCellFilter  EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "head", null, "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco\u2019s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit\u2019s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer\u2019s protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual\u2019s guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "tissue:head|cell type:neuronal|genotype:stim2a;stim2b /  ; TgHuC:GCaMP5G|age:5 dpf larvae", "GSM8215881", "GSM8215881: stim2KO  repllicate 1  scRNASeq; Danio rerio; RNA Seq", "GSM8215881 r1", "GSM8215881", "1", "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer's protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP502616", null, null, "RIS_F63_0005_P24_V11_S1_R2_001.fastq.gz RIS_F63_0005_P24_V11_S1_R1_001.fastq.gz", "fastq fastq", 19966585728.0, 155988951.0, "GSM8215881 r1", "0:28 1:100", "A:5812540331;C:4168323325;G:4507287467;T:5477684057;N:750548", 28, 100, null, null, 5812540331, 4168323325, 4507287467, 5477684057, 750548, "SRX24301541", "SRS21065460", "SRA1848620", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", 2, 0.01363, 0.87301, 0.00566, 0.36217, 0.99046, 0.78224, 0.23254, 0.57232, 28, 100, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Poland", "2024-04-18", "Larval", "Larval", "Head", "Nervous System"], [31860, "SRR28735568", "SRX24301541", "SRS21065460", "SRP502616", "PRJNA1101946", "Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]", "GSE264310", "Transcriptome Analysis", "Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests  staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum  and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL   ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer  which includes amacrine cells among others  showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b /  ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates   30 larvae per each sample and Tg control  2 replicates  30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.", "parent bioproject:PRJNA1101942", "pubmed:39424970", null, "stim2KO  repllicate 1  scRNASeq", "GSM8215881", null, "source name:head|tissue:head|cell type:neuronal|genotype:stim2a;stim2b /  ; TgHuC:GCaMP5G|age:5 dpf larvae|geo loc name:missing|collection date:missing", "stim2KO  repllicate 1  scRNASeq", "Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR  for each sample with the following parameters:   soloType CB UMI Simple    soloCBwhitelist 3M february 2018.txt [from Cell Ranger]    soloUMIlen 12    soloCBmatchWLtype 1MM multi Nbase pseudocounts    soloUMIfiltering MultiGeneUMI CR    soloUMIdedup 1MM CR    soloCellFilter  EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "head", null, "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco\u2019s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit\u2019s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer\u2019s protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual\u2019s guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "tissue:head|cell type:neuronal|genotype:stim2a;stim2b /  ; TgHuC:GCaMP5G|age:5 dpf larvae", "GSM8215881", "GSM8215881: stim2KO  repllicate 1  scRNASeq; Danio rerio; RNA Seq", "GSM8215881 r1", "GSM8215881", "1", "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer's protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP502616", null, null, "RIS_F63_0005_P24_V12_S2_R2_001.fastq.gz RIS_F63_0005_P24_V12_S2_R1_001.fastq.gz", "fastq fastq", 17678874240.0, 138116205.0, "GSM8215881 r2", "0:28 1:100", "A:5142406165;C:3696946044;G:3986515668;T:4852338487;N:667876", 28, 100, null, null, 5142406165, 3696946044, 3986515668, 4852338487, 667876, "SRX24301541", "SRS21065460", "SRA1848620", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", 2, 0.01372, 0.87988, 0.00546, 0.35939, 0.99082, 0.78042, 0.23783, 0.55977, 28, 100, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Poland", "2024-04-18", "Larval", "Larval", "Head", "Nervous System"], [31861, "SRR28735569", "SRX24301541", "SRS21065460", "SRP502616", "PRJNA1101946", "Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]", "GSE264310", "Transcriptome Analysis", "Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests  staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum  and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL   ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer  which includes amacrine cells among others  showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b /  ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates   30 larvae per each sample and Tg control  2 replicates  30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.", "parent bioproject:PRJNA1101942", "pubmed:39424970", null, "stim2KO  repllicate 1  scRNASeq", "GSM8215881", null, "source name:head|tissue:head|cell type:neuronal|genotype:stim2a;stim2b /  ; TgHuC:GCaMP5G|age:5 dpf larvae|geo loc name:missing|collection date:missing", "stim2KO  repllicate 1  scRNASeq", "Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR  for each sample with the following parameters:   soloType CB UMI Simple    soloCBwhitelist 3M february 2018.txt [from Cell Ranger]    soloUMIlen 12    soloCBmatchWLtype 1MM multi Nbase pseudocounts    soloUMIfiltering MultiGeneUMI CR    soloUMIdedup 1MM CR    soloCellFilter  EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "head", null, "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco\u2019s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit\u2019s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer\u2019s protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual\u2019s guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "tissue:head|cell type:neuronal|genotype:stim2a;stim2b /  ; TgHuC:GCaMP5G|age:5 dpf larvae", "GSM8215881", "GSM8215881: stim2KO  repllicate 1  scRNASeq; Danio rerio; RNA Seq", "GSM8215881 r1", "GSM8215881", "1", "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer's protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP502616", null, null, "RIS_F63_0005_P24_V13_S3_R2_001.fastq.gz RIS_F63_0005_P24_V13_S3_R1_001.fastq.gz", "fastq fastq", 13000627968.0, 101567406.0, "GSM8215881 r3", "0:28 1:100", "A:3777994303;C:2720540507;G:2933782069;T:3567821225;N:489864", 28, 100, null, null, 3777994303, 2720540507, 2933782069, 3567821225, 489864, "SRX24301541", "SRS21065460", "SRA1848620", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", 2, 0.01334, 0.87202, 0.0054, 0.35922, 0.98987, 0.78173, 0.25273, 0.56267, 28, 100, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Poland", "2024-04-18", "Larval", "Larval", "Head", "Nervous System"], [31862, "SRR28735570", "SRX24301541", "SRS21065460", "SRP502616", "PRJNA1101946", "Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]", "GSE264310", "Transcriptome Analysis", "Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests  staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum  and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL   ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer  which includes amacrine cells among others  showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b /  ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates   30 larvae per each sample and Tg control  2 replicates  30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.", "parent bioproject:PRJNA1101942", "pubmed:39424970", null, "stim2KO  repllicate 1  scRNASeq", "GSM8215881", null, "source name:head|tissue:head|cell type:neuronal|genotype:stim2a;stim2b /  ; TgHuC:GCaMP5G|age:5 dpf larvae|geo loc name:missing|collection date:missing", "stim2KO  repllicate 1  scRNASeq", "Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR  for each sample with the following parameters:   soloType CB UMI Simple    soloCBwhitelist 3M february 2018.txt [from Cell Ranger]    soloUMIlen 12    soloCBmatchWLtype 1MM multi Nbase pseudocounts    soloUMIfiltering MultiGeneUMI CR    soloUMIdedup 1MM CR    soloCellFilter  EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "head", null, "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco\u2019s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit\u2019s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer\u2019s protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual\u2019s guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "tissue:head|cell type:neuronal|genotype:stim2a;stim2b /  ; TgHuC:GCaMP5G|age:5 dpf larvae", "GSM8215881", "GSM8215881: stim2KO  repllicate 1  scRNASeq; Danio rerio; RNA Seq", "GSM8215881 r1", "GSM8215881", "1", "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer's protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP502616", null, null, "RIS_F63_0005_P24_V14_S4_R2_001.fastq.gz RIS_F63_0005_P24_V14_S4_R1_001.fastq.gz", "fastq fastq", 12242602112.0, 95645329.0, "GSM8215881 r4", "0:28 1:100", "A:3556852182;C:2559826440;G:2764616604;T:3360845193;N:461693", 28, 100, null, null, 3556852182, 2559826440, 2764616604, 3360845193, 461693, "SRX24301541", "SRS21065460", "SRA1848620", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", 2, 0.014, 0.87833, 0.00561, 0.35801, 0.98991, 0.78299, 0.25702, 0.57284, 28, 100, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Poland", "2024-04-18", "Larval", "Larval", "Head", "Nervous System"], [31863, "SRR28735571", "SRX24301540", "SRS21065458", "SRP502616", "PRJNA1101946", "Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]", "GSE264310", "Transcriptome Analysis", "Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests  staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum  and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL   ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer  which includes amacrine cells among others  showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b /  ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates   30 larvae per each sample and Tg control  2 replicates  30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.", "parent bioproject:PRJNA1101942", "pubmed:39424970", null, "Tg  repllicate 2  scRNASeq", "GSM8215880", null, "source name:head|tissue:head|cell type:neuronal|genotype:TgHuC:GCaMP5G|age:5 dpf larvae|geo loc name:missing|collection date:missing", "Tg  repllicate 2  scRNASeq", "Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR  for each sample with the following parameters:   soloType CB UMI Simple    soloCBwhitelist 3M february 2018.txt [from Cell Ranger]    soloUMIlen 12    soloCBmatchWLtype 1MM multi Nbase pseudocounts    soloUMIfiltering MultiGeneUMI CR    soloUMIdedup 1MM CR    soloCellFilter  EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "head", null, "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco\u2019s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit\u2019s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer\u2019s protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual\u2019s guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "tissue:head|cell type:neuronal|genotype:TgHuC:GCaMP5G|age:5 dpf larvae", "GSM8215880", "GSM8215880: Tg  repllicate 2  scRNASeq; Danio rerio; RNA Seq", "GSM8215880 r1", "GSM8215880", "1", "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer's protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP502616", null, null, "RIS_F63_0008_P24_V11_S13_R1_001.fastq.gz RIS_F63_0008_P24_V11_S13_R2_001.fastq.gz", "fastq fastq", 18512923264.0, 144632213.0, "GSM8215880 r1", "0:28 1:100", "A:5256155736;C:3979781355;G:4312684581;T:4963605318;N:696274", 28, 100, null, null, 5256155736, 3979781355, 4312684581, 4963605318, 696274, "SRX24301540", "SRS21065458", "SRA1848620", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", 2, 0.01316, 0.89227, 0.00508, 0.28873, 0.98879, 0.78218, 0.25886, 0.54866, 28, 100, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Poland", "2024-04-18", "Larval", "Larval", "Head", "Nervous System"], [31864, "SRR28735572", "SRX24301540", "SRS21065458", "SRP502616", "PRJNA1101946", "Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]", "GSE264310", "Transcriptome Analysis", "Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests  staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum  and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL   ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer  which includes amacrine cells among others  showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b /  ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates   30 larvae per each sample and Tg control  2 replicates  30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.", "parent bioproject:PRJNA1101942", "pubmed:39424970", null, "Tg  repllicate 2  scRNASeq", "GSM8215880", null, "source name:head|tissue:head|cell type:neuronal|genotype:TgHuC:GCaMP5G|age:5 dpf larvae|geo loc name:missing|collection date:missing", "Tg  repllicate 2  scRNASeq", "Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR  for each sample with the following parameters:   soloType CB UMI Simple    soloCBwhitelist 3M february 2018.txt [from Cell Ranger]    soloUMIlen 12    soloCBmatchWLtype 1MM multi Nbase pseudocounts    soloUMIfiltering MultiGeneUMI CR    soloUMIdedup 1MM CR    soloCellFilter  EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "head", null, "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco\u2019s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit\u2019s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer\u2019s protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual\u2019s guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "tissue:head|cell type:neuronal|genotype:TgHuC:GCaMP5G|age:5 dpf larvae", "GSM8215880", "GSM8215880: Tg  repllicate 2  scRNASeq; Danio rerio; RNA Seq", "GSM8215880 r1", "GSM8215880", "1", "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer's protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP502616", null, null, "RIS_F63_0008_P24_V12_S14_R1_001.fastq.gz RIS_F63_0008_P24_V12_S14_R2_001.fastq.gz", "fastq fastq", 17486730368.0, 136615081.0, "GSM8215880 r2", "0:28 1:100", "A:4977460950;C:3751371688;G:4054389958;T:4702849436;N:658336", 28, 100, null, null, 4977460950, 3751371688, 4054389958, 4702849436, 658336, "SRX24301540", "SRS21065458", "SRA1848620", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", 2, 0.01383, 0.89285, 0.00539, 0.29088, 0.98869, 0.78171, 0.23958, 0.53551, 28, 100, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Poland", "2024-04-18", "Larval", "Larval", "Head", "Nervous System"], [31865, "SRR28735573", "SRX24301540", "SRS21065458", "SRP502616", "PRJNA1101946", "Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]", "GSE264310", "Transcriptome Analysis", "Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests  staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum  and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL   ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer  which includes amacrine cells among others  showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b /  ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates   30 larvae per each sample and Tg control  2 replicates  30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.", "parent bioproject:PRJNA1101942", "pubmed:39424970", null, "Tg  repllicate 2  scRNASeq", "GSM8215880", null, "source name:head|tissue:head|cell type:neuronal|genotype:TgHuC:GCaMP5G|age:5 dpf larvae|geo loc name:missing|collection date:missing", "Tg  repllicate 2  scRNASeq", "Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR  for each sample with the following parameters:   soloType CB UMI Simple    soloCBwhitelist 3M february 2018.txt [from Cell Ranger]    soloUMIlen 12    soloCBmatchWLtype 1MM multi Nbase pseudocounts    soloUMIfiltering MultiGeneUMI CR    soloUMIdedup 1MM CR    soloCellFilter  EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "head", null, "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco\u2019s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit\u2019s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer\u2019s protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual\u2019s guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "tissue:head|cell type:neuronal|genotype:TgHuC:GCaMP5G|age:5 dpf larvae", "GSM8215880", "GSM8215880: Tg  repllicate 2  scRNASeq; Danio rerio; RNA Seq", "GSM8215880 r1", "GSM8215880", "1", "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer's protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP502616", null, null, "RIS_F63_0008_P24_V13_S15_R2_001.fastq.gz RIS_F63_0008_P24_V13_S15_R1_001.fastq.gz", "fastq fastq", 12906420736.0, 100831412.0, "GSM8215880 r3", "0:28 1:100", "A:3667742915;C:2775193040;G:3000852761;T:3462146052;N:485968", 28, 100, null, null, 3667742915, 2775193040, 3000852761, 3462146052, 485968, "SRX24301540", "SRS21065458", "SRA1848620", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", 2, 0.01323, 0.8936, 0.00513, 0.28955, 0.98859, 0.7807, 0.22054, 0.54431, 28, 100, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Poland", "2024-04-18", "Larval", "Larval", "Head", "Nervous System"], [31866, "SRR28735574", "SRX24301540", "SRS21065458", "SRP502616", "PRJNA1101946", "Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]", "GSE264310", "Transcriptome Analysis", "Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests  staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum  and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL   ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer  which includes amacrine cells among others  showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b /  ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates   30 larvae per each sample and Tg control  2 replicates  30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.", "parent bioproject:PRJNA1101942", "pubmed:39424970", null, "Tg  repllicate 2  scRNASeq", "GSM8215880", null, "source name:head|tissue:head|cell type:neuronal|genotype:TgHuC:GCaMP5G|age:5 dpf larvae|geo loc name:missing|collection date:missing", "Tg  repllicate 2  scRNASeq", "Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR  for each sample with the following parameters:   soloType CB UMI Simple    soloCBwhitelist 3M february 2018.txt [from Cell Ranger]    soloUMIlen 12    soloCBmatchWLtype 1MM multi Nbase pseudocounts    soloUMIfiltering MultiGeneUMI CR    soloUMIdedup 1MM CR    soloCellFilter  EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "head", null, "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco\u2019s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit\u2019s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer\u2019s protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual\u2019s guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "tissue:head|cell type:neuronal|genotype:TgHuC:GCaMP5G|age:5 dpf larvae", "GSM8215880", "GSM8215880: Tg  repllicate 2  scRNASeq; Danio rerio; RNA Seq", "GSM8215880 r1", "GSM8215880", "1", "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer's protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP502616", null, null, "RIS_F63_0008_P24_V14_S16_R1_001.fastq.gz RIS_F63_0008_P24_V14_S16_R2_001.fastq.gz", "fastq fastq", 13809295616.0, 107885122.0, "GSM8215880 r4", "0:28 1:100", "A:3926766598;C:2968211018;G:3214515151;T:3699280941;N:521908", 28, 100, null, null, 3926766598, 2968211018, 3214515151, 3699280941, 521908, "SRX24301540", "SRS21065458", "SRA1848620", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", 2, 0.013, 0.89441, 0.00484, 0.28706, 0.98912, 0.78027, 0.25093, 0.54201, 28, 100, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Poland", "2024-04-18", "Larval", "Larval", "Head", "Nervous System"], [31867, "SRR28735575", "SRX24301539", "SRS21065459", "SRP502616", "PRJNA1101946", "Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]", "GSE264310", "Transcriptome Analysis", "Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests  staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum  and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL   ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer  which includes amacrine cells among others  showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b /  ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates   30 larvae per each sample and Tg control  2 replicates  30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.", "parent bioproject:PRJNA1101942", "pubmed:39424970", null, "Tg  repllicate 1  scRNASeq", "GSM8215879", null, "source name:head|tissue:head|cell type:neuronal|genotype:TgHuC:GCaMP5G|age:5 dpf larvae|geo loc name:missing|collection date:missing", "Tg  repllicate 1  scRNASeq", "Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR  for each sample with the following parameters:   soloType CB UMI Simple    soloCBwhitelist 3M february 2018.txt [from Cell Ranger]    soloUMIlen 12    soloCBmatchWLtype 1MM multi Nbase pseudocounts    soloUMIfiltering MultiGeneUMI CR    soloUMIdedup 1MM CR    soloCellFilter  EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "head", null, "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco\u2019s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit\u2019s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer\u2019s protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual\u2019s guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "tissue:head|cell type:neuronal|genotype:TgHuC:GCaMP5G|age:5 dpf larvae", "GSM8215879", "GSM8215879: Tg  repllicate 1  scRNASeq; Danio rerio; RNA Seq", "GSM8215879 r1", "GSM8215879", "1", "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer's protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP502616", null, null, "RIS_F63_0007_P24_V11_S9_R2_001.fastq.gz RIS_F63_0007_P24_V11_S9_R1_001.fastq.gz", "fastq fastq", 25846470784.0, 201925553.0, "GSM8215879 r1", "0:28 1:100", "A:7418557669;C:5494387747;G:5909175364;T:7023377435;N:972569", 28, 100, null, null, 7418557669, 5494387747, 5909175364, 7023377435, 972569, "SRX24301539", "SRS21065459", "SRA1848620", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", 2, 0.01293, 0.89145, 0.00523, 0.30321, 0.98914, 0.77733, 0.2598, 0.55188, 28, 100, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Poland", "2024-04-18", "Larval", "Larval", "Head", "Nervous System"], [31868, "SRR28735576", "SRX24301539", "SRS21065459", "SRP502616", "PRJNA1101946", "Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]", "GSE264310", "Transcriptome Analysis", "Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests  staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum  and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL   ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer  which includes amacrine cells among others  showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b /  ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates   30 larvae per each sample and Tg control  2 replicates  30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.", "parent bioproject:PRJNA1101942", "pubmed:39424970", null, "Tg  repllicate 1  scRNASeq", "GSM8215879", null, "source name:head|tissue:head|cell type:neuronal|genotype:TgHuC:GCaMP5G|age:5 dpf larvae|geo loc name:missing|collection date:missing", "Tg  repllicate 1  scRNASeq", "Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR  for each sample with the following parameters:   soloType CB UMI Simple    soloCBwhitelist 3M february 2018.txt [from Cell Ranger]    soloUMIlen 12    soloCBmatchWLtype 1MM multi Nbase pseudocounts    soloUMIfiltering MultiGeneUMI CR    soloUMIdedup 1MM CR    soloCellFilter  EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "head", null, "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco\u2019s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit\u2019s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer\u2019s protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual\u2019s guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "tissue:head|cell type:neuronal|genotype:TgHuC:GCaMP5G|age:5 dpf larvae", "GSM8215879", "GSM8215879: Tg  repllicate 1  scRNASeq; Danio rerio; RNA Seq", "GSM8215879 r1", "GSM8215879", "1", "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer's protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP502616", null, null, "RIS_F63_0007_P24_V12_S10_R2_001.fastq.gz RIS_F63_0007_P24_V12_S10_R1_001.fastq.gz", "fastq fastq", 21735339264.0, 169807338.0, "GSM8215879 r2", "0:28 1:100", "A:6224752343;C:4637507813;G:4990390025;T:5881869873;N:819210", 28, 100, null, null, 6224752343, 4637507813, 4990390025, 5881869873, 819210, "SRX24301539", "SRS21065459", "SRA1848620", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", 2, 0.0129, 0.89405, 0.00501, 0.30007, 0.9892, 0.77865, 0.25727, 0.55148, 28, 100, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Poland", "2024-04-18", "Larval", "Larval", "Head", "Nervous System"], [31869, "SRR28735577", "SRX24301539", "SRS21065459", "SRP502616", "PRJNA1101946", "Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]", "GSE264310", "Transcriptome Analysis", "Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests  staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum  and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL   ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer  which includes amacrine cells among others  showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b /  ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates   30 larvae per each sample and Tg control  2 replicates  30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.", "parent bioproject:PRJNA1101942", "pubmed:39424970", null, "Tg  repllicate 1  scRNASeq", "GSM8215879", null, "source name:head|tissue:head|cell type:neuronal|genotype:TgHuC:GCaMP5G|age:5 dpf larvae|geo loc name:missing|collection date:missing", "Tg  repllicate 1  scRNASeq", "Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR  for each sample with the following parameters:   soloType CB UMI Simple    soloCBwhitelist 3M february 2018.txt [from Cell Ranger]    soloUMIlen 12    soloCBmatchWLtype 1MM multi Nbase pseudocounts    soloUMIfiltering MultiGeneUMI CR    soloUMIdedup 1MM CR    soloCellFilter  EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "head", null, "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco\u2019s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit\u2019s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer\u2019s protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual\u2019s guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "tissue:head|cell type:neuronal|genotype:TgHuC:GCaMP5G|age:5 dpf larvae", "GSM8215879", "GSM8215879: Tg  repllicate 1  scRNASeq; Danio rerio; RNA Seq", "GSM8215879 r1", "GSM8215879", "1", "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer's protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP502616", null, null, "RIS_F63_0007_P24_V13_S11_R1_001.fastq.gz RIS_F63_0007_P24_V13_S11_R2_001.fastq.gz", "fastq fastq", 143588480.0, 1121785.0, "GSM8215879 r3", "0:28 1:100", "A:41267450;C:30625679;G:32896572;T:38793424;N:5355", 28, 100, null, null, 41267450, 30625679, 32896572, 38793424, 5355, "SRX24301539", "SRS21065459", "SRA1848620", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", 2, 0.01306, 0.89063, 0.00499, 0.29993, 0.98898, 0.78084, 0.26395, 0.55218, 28, 100, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Poland", "2024-04-18", "Larval", "Larval", "Head", "Nervous System"], [31870, "SRR28735578", "SRX24301539", "SRS21065459", "SRP502616", "PRJNA1101946", "Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]", "GSE264310", "Transcriptome Analysis", "Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests  staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum  and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL   ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer  which includes amacrine cells among others  showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b /  ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates   30 larvae per each sample and Tg control  2 replicates  30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.", "parent bioproject:PRJNA1101942", "pubmed:39424970", null, "Tg  repllicate 1  scRNASeq", "GSM8215879", null, "source name:head|tissue:head|cell type:neuronal|genotype:TgHuC:GCaMP5G|age:5 dpf larvae|geo loc name:missing|collection date:missing", "Tg  repllicate 1  scRNASeq", "Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR  for each sample with the following parameters:   soloType CB UMI Simple    soloCBwhitelist 3M february 2018.txt [from Cell Ranger]    soloUMIlen 12    soloCBmatchWLtype 1MM multi Nbase pseudocounts    soloUMIfiltering MultiGeneUMI CR    soloUMIdedup 1MM CR    soloCellFilter  EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "head", null, "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco\u2019s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit\u2019s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer\u2019s protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual\u2019s guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "tissue:head|cell type:neuronal|genotype:TgHuC:GCaMP5G|age:5 dpf larvae", "GSM8215879", "GSM8215879: Tg  repllicate 1  scRNASeq; Danio rerio; RNA Seq", "GSM8215879 r1", "GSM8215879", "1", "5 dpf larvae were anesthetized by tricaine methanesulfonate MS222  a neuromuscular blocker  and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+  and L glutamine  and without xxx  and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension  the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter  which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences  Franklin Lakes  NJ. Cell viability was measured using the trypan blue staining method  and when the viability of cells was 80%  the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 \u03bcl volume. Cells were loaded according to the Chromium single cell 3\u2032 kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing  GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system  the standard manufacturer's protocol. During the encapsulation  the cells were lysed within the droplet  and they released polyadenylated RNA bound to the barcoded bead  which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines  the droplets were directly subjected to reverse transcription  the emulsion was broken  and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles  purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation \u2013 involving fragmentation  dA tailing  adapter ligation  and 12 cycle indexing PCR \u2013 was performed.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP502616", null, null, "RIS_F63_0007_P24_V14_S12_R1_001.fastq.gz RIS_F63_0007_P24_V14_S12_R2_001.fastq.gz", "fastq fastq", 16952946304.0, 132444893.0, "GSM8215879 r4", "0:28 1:100", "A:4861826090;C:3617895656;G:3887527721;T:4585054991;N:641846", 28, 100, null, null, 4861826090, 3617895656, 3887527721, 4585054991, 641846, "SRX24301539", "SRS21065459", "SRA1848620", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", 2, 0.01258, 0.89409, 0.00497, 0.2979, 0.98888, 0.77648, 0.2572, 0.55418, 28, 100, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Poland", "2024-04-18", "Larval", "Larval", "Head", "Nervous System"], [31963, "SRR28832522", "SRX24395271", "SRS21150709", "SRP504662", "PRJNA1105232", "Loss of alpha Ba crystallin  but not alpha A crystallin  increases age related cataract in the zebrafish lens", "PRJNA1105232", "Other", "The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens  possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins  alpha A  and alpha B crystallin  and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly  while zebrafish express one lens specific alpha A crystallin gene cryaa  they express two alpha B crystallin genes  with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly  unlike mouse knockout models  we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf  with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively  and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development  while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish  showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins  or in the abundant beta B1 crystallin. Overall  these findings indicate an ontogenetic shift in the functional importance of individual alpha crystallins during zebrafish lens development. Our finding that the lens specific zebrafish alpha Ba crystallin plays the leading role in preventing age related cataract adds a new twist to our understanding of vertebrate lens evolution.", null, null, null, null, "7b", null, "strain:ABC|dev stage:7 dpf|collection date:2020 10|geo loc name:USA: Oregon|sex:N/A|tissue:whole larvae|treatment:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish larvae", "7b", "7b", "10X Chromium", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP504662", null, null, "7b_concatenated_R1.fastq.gz 7b_concatenated_R2.fastq.gz", "fastq fastq", 67688938179.0, 524720451.0, "7b concatenated R1.fastq.gz", "0:28 1:101", "A:18993507272;C:15386021146;G:15634918803;T:17652028346;N:22462612", 28, 101, null, null, 18993507272, 15386021146, 15634918803, 17652028346, 22462612, "SRX24395271", "SRS21150709", "SRA1854140", "University of Oregon|Institute of Neuroscience", "University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-29", "Larval", "Larval", "Whole Organism", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 1515, "expanded_columns": [], "expandable_columns": [], "columns": ["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", 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