{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Larval\" and tissue_curation_coarse = \"Multi-system\"", "rows": [[168, "DRR075402", "DRX069316", "DRS075497", "DRP004473", "PRJDB5226", "Effects of local gut tumor on whole organismal gene expressions in zebrafish", "DRP004473", "Other", "How tumors affects whole organismal physiology remains largely unknown. To address this  we established the novel gut tumor model in zebrafish  Danio rerio. This model develops tumor at an early stage of juvenile development  when zebrafish larvae are small <4mm  enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.", null, null, "The liver of tumor fish 7dpf", "Tumor liver", "SAMD00065416", null, "sample name:6 Tumor liver 150701 Hiseq3A l3 022|tissue type:Liver", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00065416", "DRX069316", "Tumor liver", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004473", "Illumina HiSeq 2500 sequencing of SAMD00065416", null, null, null, 1091167236.0, 30310201.0, "DRR075402", "0:36", "A:272216839;C:257523620;G:259746158;T:301642763;N:37856", 36, null, null, null, 272216839, 257523620, 259746158, 301642763, 37856, "DRX069316", "DRS075497", "DRA005199", "ATR|The Thomas N. 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Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.", null, null, "The gut of tumor fish 7dpf", "Tumor gut", "SAMD00065415", null, "sample name:5 Tumor gut 150701 Hiseq3A l3 021|tissue type:Gut", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00065415", "DRX069315", "Tumor gut", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004473", "Illumina HiSeq 2500 sequencing of SAMD00065415", null, null, null, 1423792872.0, 39549802.0, "DRR075401", "0:36", "A:342328685;C:346616167;G:341519547;T:393278536;N:49937", 36, null, null, null, 342328685, 346616167, 341519547, 393278536, 49937, "DRX069315", "DRS075496", "DRA005199", "ATR|The Thomas N. 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Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.", null, null, "The remaining part of body of tumor fish 7dpf", "Tumor body", "SAMD00065414", null, "sample name:4 Tumor body 150701 Hiseq3A l3 020|tissue type:Body", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00065414", "DRX069314", "Tumor body", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004473", "Illumina HiSeq 2500 sequencing of SAMD00065414", null, null, null, 1168514964.0, 32458749.0, "DRR075400", "0:36", "A:286579925;C:275496498;G:278133055;T:328265078;N:40408", 36, null, null, null, 286579925, 275496498, 278133055, 328265078, 40408, "DRX069314", "DRS075495", "DRA005199", "ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International", "The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International", 1, 0.89927, null, 0.15051, null, 0.66714, null, 0.47579, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2018-09-19", "Larval", "Larval", "Multi-tissue", "Multi-system"], [10147, "ERR5005147", "ERX4814430", "ERS5474667", "ERP125923", "PRJEB42059", "RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "E-MTAB-9924", "Other", "DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes  however  non CG methylation mCH is also detectable in vertebrate tissues  most notably in the nervous system. In mammalian brains  it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A  ii enriched in gene bodies and repetitive elements  and iii associated with transcriptional repression. However  the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study  we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains", "ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17", null, "Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80\u00b0C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.", "6wpf rep2 RNA", "SAMEA7727294", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,", "ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727294|INSDC center alias:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:6wpf rep2 RNA|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:6wpf rep2 RNA|sex:mixed|strain:Mixed AB and Tubingen", null, null, null, null, null, null, null, null, "HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "E MTAB 9924:6wpf rep2 RNA p", "6wpf rep2 RNA p", "RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80\u00b0C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.", "Experimental Factor: age:6|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "ERP125923", "HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17", "6wpf_rep2_RNA_R1.fastq.gz 6wpf_rep2_RNA_R2.fastq.gz", "fastq fastq", 11929324428.0, 40157012.0, "E MTAB 9924:6wpf rep2 RNA R", "0:148.72 1:148.34", "A:3237937670;C:2713313024;G:2724528618;T:3251908184;N:1636932", 148, 148, null, null, 3237937670, 2713313024, 2724528618, 3251908184, 1636932, "ERX4814430", "ERS5474667", "ERA3199751", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive", 2, 0.93069, 0.93326, 0.13891, 0.13708, 0.69779, 0.71701, 0.49797, 0.49993, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2020-12-17", "Larval", "Larval", "Multi-tissue", "Multi-system"], [10148, "ERR5005146", "ERX4814429", "ERS5474666", "ERP125923", "PRJEB42059", "RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "E-MTAB-9924", "Other", "DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes  however  non CG methylation mCH is also detectable in vertebrate tissues  most notably in the nervous system. In mammalian brains  it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A  ii enriched in gene bodies and repetitive elements  and iii associated with transcriptional repression. However  the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study  we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains", "ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17", null, "Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80\u00b0C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.", "6wpf rep1 RNA", "SAMEA7727293", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,", "ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727293|INSDC center alias:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:6wpf rep1 RNA|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:6wpf rep1 RNA|sex:mixed|strain:Mixed AB and Tubingen", null, null, null, null, null, null, null, null, "HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "E MTAB 9924:6wpf rep1 RNA p", "6wpf rep1 RNA p", "RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80\u00b0C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.", "Experimental Factor: age:6|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "ERP125923", "HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17", "6wpf_rep1_RNA_R1.fastq.gz 6wpf_rep1_RNA_R2.fastq.gz", "fastq fastq", 19633084666.0, 66362913.0, "E MTAB 9924:6wpf rep1 RNA R", "0:148.10 1:147.74", "A:5348913370;C:4443593237;G:4456508875;T:5380825384;N:3243800", 148, 147, null, null, 5348913370, 4443593237, 4456508875, 5380825384, 3243800, "ERX4814429", "ERS5474666", "ERA3199751", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive", 2, 0.92182, 0.92338, 0.12138, 0.11866, 0.68499, 0.70236, 0.50638, 0.51742, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2020-12-17", "Larval", "Larval", "Multi-tissue", "Multi-system"], [10151, "ERR5005143", "ERX4814426", "ERS5474663", "ERP125923", "PRJEB42059", "RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "E-MTAB-9924", "Other", "DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes  however  non CG methylation mCH is also detectable in vertebrate tissues  most notably in the nervous system. In mammalian brains  it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A  ii enriched in gene bodies and repetitive elements  and iii associated with transcriptional repression. However  the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study  we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains", "ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17", null, "Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80\u00b0C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.", "4wpf rep2 RNA", "SAMEA7727290", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,", "ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727290|INSDC center alias:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:4wpf rep2 RNA|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:4wpf rep2 RNA|sex:mixed|strain:Mixed AB and Tubingen", null, null, null, null, null, null, null, null, "HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "E MTAB 9924:4wpf rep2 RNA p", "4wpf rep2 RNA p", "RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80\u00b0C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.", "Experimental Factor: age:4|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "ERP125923", "HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17", "4wpf_rep2_RNA_R1.fastq.gz 4wpf_rep2_RNA_R2.fastq.gz", "fastq fastq", 17862998816.0, 62733750.0, "E MTAB 9924:4wpf rep2 RNA R", "0:142.46 1:142.28", "A:4963776868;C:3947656384;G:3887833339;T:5057912943;N:5819282", 142, 142, null, null, 4963776868, 3947656384, 3887833339, 5057912943, 5819282, "ERX4814426", "ERS5474663", "ERA3199751", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive", 2, 0.9309, 0.93111, 0.1952, 0.1951, 0.70534, 0.7176, 0.50482, 0.51152, 116, 147, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2020-12-17", "Larval", "Larval", "Multi-tissue", "Multi-system"], [10152, "ERR5005142", "ERX4814425", "ERS5474662", "ERP125923", "PRJEB42059", "RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "E-MTAB-9924", "Other", "DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes  however  non CG methylation mCH is also detectable in vertebrate tissues  most notably in the nervous system. In mammalian brains  it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A  ii enriched in gene bodies and repetitive elements  and iii associated with transcriptional repression. However  the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study  we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains", "ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17", null, "Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80\u00b0C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.", "4wpf rep1 RNA", "SAMEA7727289", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,", "ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727289|INSDC center alias:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:4wpf rep1 RNA|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:4wpf rep1 RNA|sex:mixed|strain:Mixed AB and Tubingen", null, null, null, null, null, null, null, null, "HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "E MTAB 9924:4wpf rep1 RNA p", "4wpf rep1 RNA p", "RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80\u00b0C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.", "Experimental Factor: age:4|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "ERP125923", "HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17", "4wpf_rep1_RNA_R1.fastq.gz 4wpf_rep1_RNA_R2.fastq.gz", "fastq fastq", 17991275539.0, 62100394.0, "E MTAB 9924:4wpf rep1 RNA R", "0:144.97 1:144.75", "A:5021314085;C:3954412393;G:3881029269;T:5128240171;N:6279621", 144, 144, null, null, 5021314085, 3954412393, 3881029269, 5128240171, 6279621, "ERX4814425", "ERS5474662", "ERA3199751", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive", 2, 0.92732, 0.92708, 0.18879, 0.18795, 0.70171, 0.71634, 0.506, 0.50887, 150, 149, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2020-12-17", "Larval", "Larval", "Multi-tissue", "Multi-system"], [10153, "ERR5005141", "ERX4814424", "ERS5474661", "ERP125923", "PRJEB42059", "RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "E-MTAB-9924", "Other", "DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes  however  non CG methylation mCH is also detectable in vertebrate tissues  most notably in the nervous system. In mammalian brains  it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A  ii enriched in gene bodies and repetitive elements  and iii associated with transcriptional repression. However  the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study  we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains", "ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17", null, "Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80\u00b0C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.", "3wpf rep2 RNA", "SAMEA7727288", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,", "ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727288|INSDC center alias:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:3wpf rep2 RNA|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:3wpf rep2 RNA|sex:mixed|strain:Mixed AB and Tubingen", null, null, null, null, null, null, null, null, "HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "E MTAB 9924:3wpf rep2 RNA p", "3wpf rep2 RNA p", "RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80\u00b0C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.", "Experimental Factor: age:3|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "ERP125923", "HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17", "3wpf_rep2_RNA_R1.fastq.gz 3wpf_rep2_RNA_R2.fastq.gz", "fastq fastq", 22804042203.0, 76957632.0, "E MTAB 9924:3wpf rep2 RNA R", "0:148.34 1:147.98", "A:6255991654;C:5120232312;G:5136799470;T:6288581486;N:2437281", 148, 147, null, null, 6255991654, 5120232312, 5136799470, 6288581486, 2437281, "ERX4814424", "ERS5474661", "ERA3199751", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive", 2, 0.93211, 0.93322, 0.20907, 0.2056, 0.6983, 0.71652, 0.53448, 0.5352, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2020-12-17", "Larval", "Larval", "Multi-tissue", "Multi-system"], [10154, "ERR5005140", "ERX4814423", "ERS5474660", "ERP125923", "PRJEB42059", "RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "E-MTAB-9924", "Other", "DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes  however  non CG methylation mCH is also detectable in vertebrate tissues  most notably in the nervous system. In mammalian brains  it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A  ii enriched in gene bodies and repetitive elements  and iii associated with transcriptional repression. However  the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study  we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains", "ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17", null, "Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80\u00b0C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.", "3wpf rep1 RNA", "SAMEA7727287", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,", "ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727287|INSDC center alias:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:3wpf rep1 RNA|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:3wpf rep1 RNA|sex:mixed|strain:Mixed AB and Tubingen", null, null, null, null, null, null, null, null, "HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "E MTAB 9924:3wpf rep1 RNA p", "3wpf rep1 RNA p", "RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80\u00b0C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.", "Experimental Factor: age:3|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "ERP125923", "HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17", "3wpf_rep1_RNA_R1.fastq.gz 3wpf_rep1_RNA_R2.fastq.gz", "fastq fastq", 25549987003.0, 86260528.0, "E MTAB 9924:3wpf rep1 RNA R", "0:148.28 1:147.91", "A:6961927451;C:5786809647;G:5798882444;T:6999483818;N:2883643", 148, 147, null, null, 6961927451, 5786809647, 5798882444, 6999483818, 2883643, "ERX4814423", "ERS5474660", "ERA3199751", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive", 2, 0.93267, 0.93467, 0.20372, 0.20263, 0.69252, 0.70962, 0.53426, 0.54087, 149, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2020-12-17", "Larval", "Larval", "Multi-tissue", "Multi-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"], [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"], [24854, "SRR25519420", "SRX21249697", "SRS18503946", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  AR42 TFA 4  3dpf", "GSM7681266", null, "source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing", "zebrafish  AR42 TFA 4  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:AR 42 treated larvae with TFA modeling", "GSM7681266", "GSM7681266: zebrafish  AR42 TFA 4  3dpf; Danio rerio; RNA Seq", "GSM7681266 r1", "GSM7681266", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "AR42_TFA_4.R1.fq.gz AR42_TFA_4.R2.fq.gz", "fastq fastq", 9896772900.0, 32989243.0, "GSM7681266 r1", "0:150 1:150", "A:2382403653;C:2457377213;G:2470646159;T:2586345875;N:0", 150, 150, null, null, 2382403653, 2457377213, 2470646159, 2586345875, 0, "SRX21249697", "SRS18503946", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.70537, 0.88934, 0.03159, 0.04209, 0.78013, 0.75416, 0.50713, 0.45138, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24855, "SRR25519421", "SRX21249696", "SRS18503945", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  AR42 TFA 3  3dpf", "GSM7681265", null, "source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing", "zebrafish  AR42 TFA 3  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:AR 42 treated larvae with TFA modeling", "GSM7681265", "GSM7681265: zebrafish  AR42 TFA 3  3dpf; Danio rerio; RNA Seq", "GSM7681265 r1", "GSM7681265", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "AR42_TFA_3.R1.fq.gz AR42_TFA_3.R2.fq.gz", "fastq fastq", 10265927100.0, 34219757.0, "GSM7681265 r1", "0:150 1:150", "A:2473552302;C:2548535087;G:2562873160;T:2680966551;N:0", 150, 150, null, null, 2473552302, 2548535087, 2562873160, 2680966551, 0, "SRX21249696", "SRS18503945", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.70516, 0.88765, 0.03163, 0.04168, 0.7782, 0.75083, 0.50851, 0.45305, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24856, "SRR25519422", "SRX21249695", "SRS18503944", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  AR42 TFA 2  3dpf", "GSM7681264", null, "source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing", "zebrafish  AR42 TFA 2  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:AR 42 treated larvae with TFA modeling", "GSM7681264", "GSM7681264: zebrafish  AR42 TFA 2  3dpf; Danio rerio; RNA Seq", "GSM7681264 r1", "GSM7681264", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "AR42_TFA_2.R2.fq.gz AR42_TFA_2.R1.fq.gz", "fastq fastq", 10003398900.0, 33344663.0, "GSM7681264 r1", "0:150 1:150", "A:2409580340;C:2483650756;G:2497057051;T:2613110753;N:0", 150, 150, null, null, 2409580340, 2483650756, 2497057051, 2613110753, 0, "SRX21249695", "SRS18503944", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.70787, 0.89158, 0.03203, 0.04194, 0.77851, 0.75108, 0.5072, 0.45508, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24857, "SRR25519423", "SRX21249694", "SRS18503943", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  AR42 TFA 1  3dpf", "GSM7681263", null, "source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing", "zebrafish  AR42 TFA 1  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:AR 42 treated larvae with TFA modeling", "GSM7681263", "GSM7681263: zebrafish  AR42 TFA 1  3dpf; Danio rerio; RNA Seq", "GSM7681263 r1", "GSM7681263", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "AR42_TFA_1.R1.fq.gz AR42_TFA_1.R2.fq.gz", "fastq fastq", 7420308900.0, 24734363.0, "GSM7681263 r1", "0:150 1:150", "A:1791092728;C:1841012408;G:1852583633;T:1935620131;N:0", 150, 150, null, null, 1791092728, 1841012408, 1852583633, 1935620131, 0, "SRX21249694", "SRS18503943", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.69668, 0.87862, 0.03153, 0.04215, 0.77463, 0.74949, 0.50657, 0.45971, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24858, "SRR25519424", "SRX21249693", "SRS18503942", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  DMSO TFA 4  3dpf", "GSM7681262", null, "source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing", "zebrafish  DMSO TFA 4  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:DMSO treated larvae with TFA modeling", "GSM7681262", "GSM7681262: zebrafish  DMSO TFA 4  3dpf; Danio rerio; RNA Seq", "GSM7681262 r1", "GSM7681262", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "DMSO_TFA_4.R1.fq.gz DMSO_TFA_4.R2.fq.gz", "fastq fastq", 10178474100.0, 33928247.0, "GSM7681262 r1", "0:150 1:150", "A:2452172460;C:2526571372;G:2532799116;T:2666931152;N:0", 150, 150, null, null, 2452172460, 2526571372, 2532799116, 2666931152, 0, "SRX21249693", "SRS18503942", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.72132, 0.91072, 0.03161, 0.04366, 0.77709, 0.75016, 0.516, 0.45312, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24859, "SRR25519425", "SRX21249692", "SRS18503941", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  DMSO TFA 3  3dpf", "GSM7681261", null, "source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing", "zebrafish  DMSO TFA 3  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:DMSO treated larvae with TFA modeling", "GSM7681261", "GSM7681261: zebrafish  DMSO TFA 3  3dpf; Danio rerio; RNA Seq", "GSM7681261 r1", "GSM7681261", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "DMSO_TFA_3.R1.fq.gz DMSO_TFA_3.R2.fq.gz", "fastq fastq", 9483201300.0, 31610671.0, "GSM7681261 r1", "0:150 1:150", "A:2282797855;C:2354211318;G:2361918927;T:2484273200;N:0", 150, 150, null, null, 2282797855, 2354211318, 2361918927, 2484273200, 0, "SRX21249692", "SRS18503941", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.71779, 0.90757, 0.03224, 0.04329, 0.77853, 0.74862, 0.51128, 0.44891, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24860, "SRR25519426", "SRX21249691", "SRS18503940", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  DMSO TFA 2  3dpf", "GSM7681260", null, "source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing", "zebrafish  DMSO TFA 2  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:DMSO treated larvae with TFA modeling", "GSM7681260", "GSM7681260: zebrafish  DMSO TFA 2  3dpf; Danio rerio; RNA Seq", "GSM7681260 r1", "GSM7681260", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "DMSO_TFA_2.R1.fq.gz DMSO_TFA_2.R2.fq.gz", "fastq fastq", 9372641700.0, 31242139.0, "GSM7681260 r1", "0:150 1:150", "A:2255045813;C:2327185536;G:2333956274;T:2456454077;N:0", 150, 150, null, null, 2255045813, 2327185536, 2333956274, 2456454077, 0, "SRX21249691", "SRS18503940", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.71913, 0.91061, 0.0318, 0.04251, 0.7778, 0.74907, 0.51295, 0.45006, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24861, "SRR25519427", "SRX21249690", "SRS18503939", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  DMSO TFA 1  3dpf", "GSM7681259", null, "source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing", "zebrafish  DMSO TFA 1  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:DMSO treated larvae with TFA modeling", "GSM7681259", "GSM7681259: zebrafish  DMSO TFA 1  3dpf; Danio rerio; RNA Seq", "GSM7681259 r1", "GSM7681259", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "DMSO_TFA_1.R1.fq.gz DMSO_TFA_1.R2.fq.gz", "fastq fastq", 8665981200.0, 28886604.0, "GSM7681259 r1", "0:150 1:150", "A:2086560929;C:2153111953;G:2157203992;T:2269104326;N:0", 150, 150, null, null, 2086560929, 2153111953, 2157203992, 2269104326, 0, "SRX21249690", "SRS18503939", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.71996, 0.90816, 0.03211, 0.04297, 0.77739, 0.75097, 0.5122, 0.452, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24862, "SRR25519428", "SRX21249689", "SRS18503938", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  AR42 4  3dpf", "GSM7681258", null, "source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing", "zebrafish  AR42 4  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:AR 42 treated larvae without xxx modeling", "GSM7681258", "GSM7681258: zebrafish  AR42 4  3dpf; Danio rerio; RNA Seq", "GSM7681258 r1", "GSM7681258", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "AR42_4.R1.fq.gz AR42_4.R2.fq.gz", "fastq fastq", 10199154900.0, 33997183.0, "GSM7681258 r1", "0:150 1:150", "A:2461755295;C:2524481077;G:2536143078;T:2676775450;N:0", 150, 150, null, null, 2461755295, 2524481077, 2536143078, 2676775450, 0, "SRX21249689", "SRS18503938", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.70676, 0.89456, 0.031, 0.04108, 0.77508, 0.747, 0.44642, 0.47521, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24863, "SRR25519429", "SRX21249688", "SRS18503937", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  AR42 3  3dpf", "GSM7681257", null, "source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing", "zebrafish  AR42 3  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:AR 42 treated larvae without xxx modeling", "GSM7681257", "GSM7681257: zebrafish  AR42 3  3dpf; Danio rerio; RNA Seq", "GSM7681257 r1", "GSM7681257", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "AR42_3.R1.fq.gz AR42_3.R2.fq.gz", "fastq fastq", 9953498100.0, 33178327.0, "GSM7681257 r1", "0:150 1:150", "A:2400858967;C:2463285586;G:2477369817;T:2611983730;N:0", 150, 150, null, null, 2400858967, 2463285586, 2477369817, 2611983730, 0, "SRX21249688", "SRS18503937", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.70865, 0.89517, 0.03101, 0.04127, 0.77325, 0.74679, 0.50253, 0.50409, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24864, "SRR25519430", "SRX21249687", "SRS18503936", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  AR42 2  3dpf", "GSM7681256", null, "source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing", "zebrafish  AR42 2  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:AR 42 treated larvae without xxx modeling", "GSM7681256", "GSM7681256: zebrafish  AR42 2  3dpf; Danio rerio; RNA Seq", "GSM7681256 r1", "GSM7681256", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "AR42_2.R1.fq.gz AR42_2.R2.fq.gz", "fastq fastq", 10005489000.0, 33351630.0, "GSM7681256 r1", "0:150 1:150", "A:2413672248;C:2477611702;G:2491304598;T:2622900452;N:0", 150, 150, null, null, 2413672248, 2477611702, 2491304598, 2622900452, 0, "SRX21249687", "SRS18503936", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.70639, 0.89204, 0.03035, 0.04087, 0.77502, 0.74955, 0.50558, 0.50545, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24865, "SRR25519431", "SRX21249686", "SRS18503935", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  AR42 1  3dpf", "GSM7681255", null, "source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing", "zebrafish  AR42 1  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:AR 42 treated larvae without xxx modeling", "GSM7681255", "GSM7681255: zebrafish  AR42 1  3dpf; Danio rerio; RNA Seq", "GSM7681255 r1", "GSM7681255", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "AR42_1.R1.fq.gz AR42_1.R2.fq.gz", "fastq fastq", 9698587800.0, 32328626.0, "GSM7681255 r1", "0:150 1:150", "A:2337968859;C:2400315331;G:2416067610;T:2544236000;N:0", 150, 150, null, null, 2337968859, 2400315331, 2416067610, 2544236000, 0, "SRX21249686", "SRS18503935", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.70903, 0.89448, 0.02976, 0.04032, 0.77583, 0.74935, 0.50747, 0.5081, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24866, "SRR25519432", "SRX21249685", "SRS18503934", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  DMSO 4  3dpf", "GSM7681254", null, "source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing", "zebrafish  DMSO 4  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:DMSO treated larvae without xxx modeling", "GSM7681254", "GSM7681254: zebrafish  DMSO 4  3dpf; Danio rerio; RNA Seq", "GSM7681254 r1", "GSM7681254", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "DMSO_4.R1.fq.gz DMSO_4.R2.fq.gz", "fastq fastq", 9083670000.0, 30278900.0, "GSM7681254 r1", "0:150 1:150", "A:2191941100;C:2247936730;G:2258913579;T:2384878591;N:0", 150, 150, null, null, 2191941100, 2247936730, 2258913579, 2384878591, 0, "SRX21249685", "SRS18503934", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.71071, 0.90457, 0.03362, 0.04688, 0.77106, 0.74357, 0.50842, 0.50975, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24867, "SRR25519433", "SRX21249684", "SRS18503933", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  DMSO 3  3dpf", "GSM7681253", null, "source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing", "zebrafish  DMSO 3  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:DMSO treated larvae without xxx modeling", "GSM7681253", "GSM7681253: zebrafish  DMSO 3  3dpf; Danio rerio; RNA Seq", "GSM7681253 r1", "GSM7681253", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "DMSO_3.R2.fq.gz DMSO_3.R1.fq.gz", "fastq fastq", 9394455000.0, 31314850.0, "GSM7681253 r1", "0:150 1:150", "A:2266296733;C:2324081714;G:2335347043;T:2468729510;N:0", 150, 150, null, null, 2266296733, 2324081714, 2335347043, 2468729510, 0, "SRX21249684", "SRS18503933", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.70975, 0.90445, 0.03329, 0.04594, 0.77005, 0.7417, 0.51188, 0.5163, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24868, "SRR25519434", "SRX21249683", "SRS18503932", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  DMSO 2  3dpf", "GSM7681252", null, "source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing", "zebrafish  DMSO 2  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:DMSO treated larvae without xxx modeling", "GSM7681252", "GSM7681252: zebrafish  DMSO 2  3dpf; Danio rerio; RNA Seq", "GSM7681252 r1", "GSM7681252", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "DMSO_2.R1.fq.gz DMSO_2.R2.fq.gz", "fastq fastq", 9157453500.0, 30524845.0, "GSM7681252 r1", "0:150 1:150", "A:2209331568;C:2266614182;G:2273923578;T:2407584172;N:0", 150, 150, null, null, 2209331568, 2266614182, 2273923578, 2407584172, 0, "SRX21249683", "SRS18503932", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.70922, 0.90538, 0.03379, 0.04616, 0.7723, 0.74213, 0.50839, 0.50803, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24869, "SRR25519435", "SRX21249682", "SRS18503931", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  DMSO 1  3dpf", "GSM7681251", null, "source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing", "zebrafish  DMSO 1  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:DMSO treated larvae without xxx modeling", "GSM7681251", "GSM7681251: zebrafish  DMSO 1  3dpf; Danio rerio; RNA Seq", "GSM7681251 r1", "GSM7681251", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "DMSO_1.R2.fq.gz DMSO_1.R1.fq.gz", "fastq fastq", 8769040200.0, 29230134.0, "GSM7681251 r1", "0:150 1:150", "A:2114427483;C:2170929931;G:2179906163;T:2303776623;N:0", 150, 150, null, null, 2114427483, 2170929931, 2179906163, 2303776623, 0, "SRX21249682", "SRS18503931", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.71002, 0.9037, 0.0335, 0.04604, 0.77155, 0.74308, 0.51339, 0.50801, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "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"], [26518, "SRR26050763", "SRX21767119", "SRS18873424", "SRP460207", "PRJNA1016321", "The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis", "GSE243072", "Transcriptome Analysis", "Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 mutants  72hpf  biological replicate 4  cranial sox10+ cells", "GSM7778660", null, "source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / |geo loc name:missing|collection date:missing", "psmb1 mutants  72hpf  biological replicate 4  cranial sox10+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial sox10+ cells neural crest/chondrocytes", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / ", "GSM7778660", "GSM7778660: psmb1 mutants  72hpf  biological replicate 4  cranial sox10+ cells; Danio rerio; RNA Seq", "GSM7778660 r1", "GSM7778660", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP460207", null, "loader:fastq load.py", "sox10_M4_R1_001.fastq.gz sox10_M4_R2_001.fastq.gz", "fastq fastq", 17203316400.0, 57344388.0, "GSM7778660 r1", "0:150 1:150", "A:4557769784;C:4038080087;G:4028545423;T:4578857383;N:63723", 150, 150, null, null, 4557769784, 4038080087, 4028545423, 4578857383, 63723, "SRX21767119", "SRS18873424", "SRA1711572", "BWH", "BWH", 2, 0.93924, 0.93866, 0.10703, 0.1068, 0.70597, 0.70508, 0.52195, 0.52023, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "nextera", "bulk", "bulk", "bulk", null, "United States", "2023-09-13", "Larval", "Larval", "Multi-tissue", "Multi-system"], [26519, "SRR26050764", "SRX21767118", "SRS18873423", "SRP460207", "PRJNA1016321", "The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis", "GSE243072", "Transcriptome Analysis", "Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 mutants  72hpf  biological replicate 3  cranial sox10+ cells", "GSM7778659", null, "source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / |geo loc name:missing|collection date:missing", "psmb1 mutants  72hpf  biological replicate 3  cranial sox10+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial sox10+ cells neural crest/chondrocytes", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / ", "GSM7778659", "GSM7778659: psmb1 mutants  72hpf  biological replicate 3  cranial sox10+ cells; Danio rerio; RNA Seq", "GSM7778659 r1", "GSM7778659", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP460207", null, "loader:fastq load.py", "sox10_M3_R1_001.fastq.gz sox10_M3_R2_001.fastq.gz", "fastq fastq", 16490564400.0, 54968548.0, "GSM7778659 r1", "0:150 1:150", "A:4465032867;C:3767540674;G:3755500192;T:4502428180;N:62487", 150, 150, null, null, 4465032867, 3767540674, 3755500192, 4502428180, 62487, "SRX21767118", "SRS18873423", "SRA1711572", "BWH", "BWH", 2, 0.92805, 0.92792, 0.14244, 0.14225, 0.69639, 0.69757, 0.52133, 0.52056, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "nextera", "bulk", "bulk", "bulk", null, "United States", "2023-09-13", "Larval", "Larval", "Multi-tissue", "Multi-system"], [26520, "SRR26050765", "SRX21767117", "SRS18873422", "SRP460207", "PRJNA1016321", "The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis", "GSE243072", "Transcriptome Analysis", "Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 mutants  72hpf  biological replicate 1  cranial sox10+ cells", "GSM7778658", null, "source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / |geo loc name:missing|collection date:missing", "psmb1 mutants  72hpf  biological replicate 1  cranial sox10+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial sox10+ cells neural crest/chondrocytes", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / ", "GSM7778658", "GSM7778658: psmb1 mutants  72hpf  biological replicate 1  cranial sox10+ cells; Danio rerio; RNA Seq", "GSM7778658 r1", "GSM7778658", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP460207", null, "loader:fastq load.py", "sox10_M1_R1_001.fastq.gz sox10_M1_R2_001.fastq.gz", "fastq fastq", 14363136600.0, 47877122.0, "GSM7778658 r1", "0:150 1:150", "A:3843987690;C:3329370255;G:3310959116;T:3878765025;N:54514", 150, 150, null, null, 3843987690, 3329370255, 3310959116, 3878765025, 54514, "SRX21767117", "SRS18873422", "SRA1711572", "BWH", "BWH", 2, 0.92722, 0.92625, 0.11695, 0.11644, 0.69611, 0.6969, 0.52036, 0.522, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "nextera", "bulk", "bulk", "bulk", null, "United States", "2023-09-13", "Larval", "Larval", "Multi-tissue", "Multi-system"], [26521, "SRR26050766", "SRX21767116", "SRS18873421", "SRP460207", "PRJNA1016321", "The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis", "GSE243072", "Transcriptome Analysis", "Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 wild type/heterozygous 72hpf  biological replicate 4  cranial sox10+ cells", "GSM7778657", null, "source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing", "psmb1 wild type/heterozygous 72hpf  biological replicate 4  cranial sox10+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial sox10+ cells neural crest/chondrocytes", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ ", "GSM7778657", "GSM7778657: psmb1 wild type/heterozygous 72hpf  biological replicate 4  cranial sox10+ cells; Danio rerio; RNA Seq", "GSM7778657 r1", "GSM7778657", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP460207", null, "loader:fastq load.py", "sox10_WH4_R1_001.fastq.gz sox10_WH4_R2_001.fastq.gz", "fastq fastq", 14383303200.0, 47944344.0, "GSM7778657 r1", "0:150 1:150", "A:3825787510;C:3356860561;G:3322388892;T:3878211922;N:54315", 150, 150, null, null, 3825787510, 3356860561, 3322388892, 3878211922, 54315, "SRX21767116", "SRS18873421", "SRA1711572", "BWH", "BWH", 2, 0.93157, 0.93024, 0.09771, 0.09735, 0.7177, 0.71829, 0.52664, 0.52877, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "nextera", "bulk", "bulk", "bulk", null, "United States", "2023-09-13", "Larval", "Larval", "Multi-tissue", "Multi-system"], [26522, "SRR26050767", "SRX21767115", "SRS18873420", "SRP460207", "PRJNA1016321", "The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis", "GSE243072", "Transcriptome Analysis", "Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 wild type/heterozygous 72hpf  biological replicate 3  cranial sox10+ cells", "GSM7778656", null, "source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing", "psmb1 wild type/heterozygous 72hpf  biological replicate 3  cranial sox10+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial sox10+ cells neural crest/chondrocytes", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ ", "GSM7778656", "GSM7778656: psmb1 wild type/heterozygous 72hpf  biological replicate 3  cranial sox10+ cells; Danio rerio; RNA Seq", "GSM7778656 r1", "GSM7778656", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP460207", null, "loader:fastq load.py", "sox10_WH3_R1_001.fastq.gz sox10_WH3_R2_001.fastq.gz", "fastq fastq", 13772364600.0, 45907882.0, "GSM7778656 r1", "0:150 1:150", "A:3599468762;C:3277366623;G:3241941715;T:3653534992;N:52508", 150, 150, null, null, 3599468762, 3277366623, 3241941715, 3653534992, 52508, "SRX21767115", "SRS18873420", "SRA1711572", "BWH", "BWH", 2, 0.94023, 0.93961, 0.07684, 0.07628, 0.70654, 0.70682, 0.50963, 0.51111, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "nextera", "bulk", "bulk", "bulk", null, "United States", "2023-09-13", "Larval", "Larval", "Multi-tissue", "Multi-system"], [26523, "SRR26050768", "SRX21767114", "SRS18873419", "SRP460207", "PRJNA1016321", "The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis", "GSE243072", "Transcriptome Analysis", "Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 wild type/heterozygous 72hpf  biological replicate 2  cranial sox10+ cells", "GSM7778655", null, "source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing", "psmb1 wild type/heterozygous 72hpf  biological replicate 2  cranial sox10+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial sox10+ cells neural crest/chondrocytes", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ ", "GSM7778655", "GSM7778655: psmb1 wild type/heterozygous 72hpf  biological replicate 2  cranial sox10+ cells; Danio rerio; RNA Seq", "GSM7778655 r1", "GSM7778655", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP460207", null, "loader:fastq load.py", "sox10_WH2_R1_001.fastq.gz sox10_WH2_R2_001.fastq.gz", "fastq fastq", 15229813200.0, 50766044.0, "GSM7778655 r1", "0:150 1:150", "A:4029459993;C:3570808650;G:3534029380;T:4095461104;N:54073", 150, 150, null, null, 4029459993, 3570808650, 3534029380, 4095461104, 54073, "SRX21767114", "SRS18873419", "SRA1711572", "BWH", "BWH", 2, 0.93346, 0.93269, 0.13006, 0.13022, 0.70094, 0.70007, 0.51067, 0.50945, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "nextera", "bulk", "bulk", "bulk", null, "United States", "2023-09-13", "Larval", "Larval", "Multi-tissue", "Multi-system"], [26524, "SRR26050769", "SRX21767113", "SRS18873418", "SRP460207", "PRJNA1016321", "The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis", "GSE243072", "Transcriptome Analysis", "Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 wild type/heterozygous 72hpf  biological replicate 1  cranial sox10+ cells", "GSM7778654", null, "source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing", "psmb1 wild type/heterozygous 72hpf  biological replicate 1  cranial sox10+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial sox10+ cells neural crest/chondrocytes", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ ", "GSM7778654", "GSM7778654: psmb1 wild type/heterozygous 72hpf  biological replicate 1  cranial sox10+ cells; Danio rerio; RNA Seq", "GSM7778654 r1", "GSM7778654", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP460207", null, "loader:fastq load.py", "sox10_WH1_R1_001.fastq.gz sox10_WH1_R2_001.fastq.gz", "fastq fastq", 13483692600.0, 44945642.0, "GSM7778654 r1", "0:150 1:150", "A:3567731759;C:3163438678;G:3137216449;T:3615254758;N:50956", 150, 150, null, null, 3567731759, 3163438678, 3137216449, 3615254758, 50956, "SRX21767113", "SRS18873418", "SRA1711572", "BWH", "BWH", 2, 0.92459, 0.92408, 0.11911, 0.11956, 0.7027, 0.70264, 0.50884, 0.50322, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "nextera", "bulk", "bulk", "bulk", null, "United States", "2023-09-13", "Larval", "Larval", "Multi-tissue", "Multi-system"], [29894, "SRR30873028", "SRX26270368", "SRS22808226", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  6 dpf  rep15", "GSM8553345", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i wild types|geo loc name:missing|collection date:missing", "arid1b  6 dpf  rep15", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i wild types", "GSM8553345", "GSM8553345: arid1b  6 dpf  rep15; Danio rerio; RNA Seq", "GSM8553345 r1", "GSM8553345", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, null, "arid1b-195d50i-wt_AR28_S28_R1_001.fastq.gz", "fastq", 4135380800.0, 41353808.0, "GSM8553345 r1", "0:100", "A:1084939463;C:1011079577;G:970891275;T:1068398012;N:72473", 100, null, null, null, 1084939463, 1011079577, 970891275, 1068398012, 72473, "SRX26270368", "SRS22808226", "SRA1985473", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-10-03", "Larval", "Larval", "Multi-tissue", "Multi-system"], [29895, "SRR30873029", "SRX26270367", "SRS22808225", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  6 dpf  rep14", "GSM8553344", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i wild types|geo loc name:missing|collection date:missing", "arid1b  6 dpf  rep14", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i wild types", "GSM8553344", "GSM8553344: arid1b  6 dpf  rep14; Danio rerio; RNA Seq", "GSM8553344 r1", "GSM8553344", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, null, "arid1b-195d50i-wt_AR27_S27_R1_001.fastq.gz", "fastq", 6224312000.0, 62243120.0, "GSM8553344 r1", "0:100", "A:1606079574;C:1540033115;G:1483199092;T:1594888859;N:111360", 100, null, null, null, 1606079574, 1540033115, 1483199092, 1594888859, 111360, "SRX26270367", "SRS22808225", "SRA1985473", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-10-03", "Larval", "Larval", "Multi-tissue", "Multi-system"], [29896, "SRR30873030", "SRX26270366", "SRS22808224", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  6 dpf  rep13", "GSM8553343", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i wild types|geo loc name:missing|collection date:missing", "arid1b  6 dpf  rep13", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i wild types", "GSM8553343", "GSM8553343: arid1b  6 dpf  rep13; Danio rerio; RNA Seq", "GSM8553343 r1", "GSM8553343", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, null, "arid1b-195d50i-wt_AR26_S26_R1_001.fastq.gz", "fastq", 4549812900.0, 45498129.0, "GSM8553343 r1", "0:100", "A:1188852707;C:1130004381;G:1033560381;T:1197314769;N:80662", 100, null, null, null, 1188852707, 1130004381, 1033560381, 1197314769, 80662, "SRX26270366", "SRS22808224", "SRA1985473", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-10-03", "Larval", "Larval", "Multi-tissue", "Multi-system"], [29897, "SRR30873031", "SRX26270365", "SRS22808223", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  6 dpf  rep12", "GSM8553342", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i wild types|geo loc name:missing|collection date:missing", "arid1b  6 dpf  rep12", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i wild types", "GSM8553342", "GSM8553342: arid1b  6 dpf  rep12; Danio rerio; RNA Seq", "GSM8553342 r1", "GSM8553342", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, null, "arid1b-195d50i-wt_AR25_S25_R1_001.fastq.gz", "fastq", 4879728400.0, 48797284.0, "GSM8553342 r1", "0:100", "A:1257198257;C:1231843411;G:1157132375;T:1233469179;N:85178", 100, null, null, null, 1257198257, 1231843411, 1157132375, 1233469179, 85178, "SRX26270365", "SRS22808223", "SRA1985473", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-10-03", "Larval", "Larval", "Multi-tissue", "Multi-system"], [29898, "SRR30873032", "SRX26270364", "SRS22808222", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  6 dpf  rep11", "GSM8553341", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i wild types|geo loc name:missing|collection date:missing", "arid1b  6 dpf  rep11", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i wild types", "GSM8553341", "GSM8553341: arid1b  6 dpf  rep11; Danio rerio; RNA Seq", "GSM8553341 r1", "GSM8553341", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, null, "arid1b-195d50i-wt_AR24_S24_R1_001.fastq.gz", "fastq", 4082165400.0, 40821654.0, "GSM8553341 r1", "0:100", "A:1040984378;C:1022942149;G:978845633;T:1039318707;N:74533", 100, null, null, null, 1040984378, 1022942149, 978845633, 1039318707, 74533, "SRX26270364", "SRS22808222", "SRA1985473", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-10-03", "Larval", "Larval", "Multi-tissue", "Multi-system"], [29899, "SRR30873033", "SRX26270363", "SRS22808221", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  6 dpf  rep10", "GSM8553340", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i homozygous|geo loc name:missing|collection date:missing", "arid1b  6 dpf  rep10", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i homozygous", "GSM8553340", "GSM8553340: arid1b  6 dpf  rep10; Danio rerio; RNA Seq", "GSM8553340 r1", "GSM8553340", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, null, "arid1b-195d50i-hom_AR23_S23_R1_001.fastq.gz", "fastq", 4661017700.0, 46610177.0, "GSM8553340 r1", "0:100", "A:1238725482;C:1138186288;G:1061058641;T:1222964445;N:82844", 100, null, null, null, 1238725482, 1138186288, 1061058641, 1222964445, 82844, "SRX26270363", "SRS22808221", "SRA1985473", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-10-03", "Larval", "Larval", "Multi-tissue", "Multi-system"], [29900, "SRR30873034", "SRX26270362", "SRS22808220", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  6 dpf  rep9", "GSM8553339", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i homozygous|geo loc name:missing|collection date:missing", "arid1b  6 dpf  rep9", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i homozygous", "GSM8553339", "GSM8553339: arid1b  6 dpf  rep9; Danio rerio; RNA Seq", "GSM8553339 r1", "GSM8553339", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, null, "arid1b-195d50i-hom_AR22_S22_R1_001.fastq.gz", "fastq", 4221752400.0, 42217524.0, "GSM8553339 r1", "0:100", "A:1065652742;C:1071696614;G:1016007642;T:1068321142;N:74260", 100, null, null, null, 1065652742, 1071696614, 1016007642, 1068321142, 74260, "SRX26270362", "SRS22808220", "SRA1985473", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-10-03", "Larval", "Larval", "Multi-tissue", "Multi-system"], [29901, "SRR30873035", "SRX26270361", "SRS22808219", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  6 dpf  rep8", "GSM8553338", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i homozygous|geo loc name:missing|collection date:missing", "arid1b  6 dpf  rep8", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i homozygous", "GSM8553338", "GSM8553338: arid1b  6 dpf  rep8; Danio rerio; RNA Seq", "GSM8553338 r1", "GSM8553338", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, null, "arid1b-195d50i-hom_AR21_S21_R1_001.fastq.gz", "fastq", 4432057900.0, 44320579.0, "GSM8553338 r1", "0:100", "A:1141942260;C:1108384050;G:1058194972;T:1123456708;N:79910", 100, null, null, null, 1141942260, 1108384050, 1058194972, 1123456708, 79910, "SRX26270361", "SRS22808219", "SRA1985473", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-10-03", "Larval", "Larval", "Multi-tissue", "Multi-system"], [29902, "SRR30873036", "SRX26270360", "SRS22808218", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  6 dpf  rep7", "GSM8553337", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i homozygous|geo loc name:missing|collection date:missing", "arid1b  6 dpf  rep7", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i homozygous", "GSM8553337", "GSM8553337: arid1b  6 dpf  rep7; Danio rerio; RNA Seq", "GSM8553337 r1", "GSM8553337", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, null, "arid1b-195d50i-hom_AR20_S20_R1_001.fastq.gz", "fastq", 4445102100.0, 44451021.0, "GSM8553337 r1", "0:100", "A:1155131497;C:1102948564;G:1044423066;T:1142521451;N:77522", 100, null, null, null, 1155131497, 1102948564, 1044423066, 1142521451, 77522, "SRX26270360", "SRS22808218", "SRA1985473", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-10-03", "Larval", "Larval", "Multi-tissue", "Multi-system"], [29903, "SRR30873037", "SRX26270359", "SRS22808217", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  6 dpf  rep6", "GSM8553336", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i homozygous|geo loc name:missing|collection date:missing", "arid1b  6 dpf  rep6", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i homozygous", "GSM8553336", "GSM8553336: arid1b  6 dpf  rep6; Danio rerio; RNA Seq", "GSM8553336 r1", "GSM8553336", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, null, "arid1b-195d50i-hom_AR19_S19_R1_001.fastq.gz", "fastq", 4466739200.0, 44667392.0, "GSM8553336 r1", "0:100", "A:1142963908;C:1130243443;G:1069626640;T:1123824589;N:80620", 100, null, null, null, 1142963908, 1130243443, 1069626640, 1123824589, 80620, "SRX26270359", "SRS22808217", "SRA1985473", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-10-03", "Larval", "Larval", "Multi-tissue", "Multi-system"], [29904, "SRR30873038", "SRX26270358", "SRS22808216", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  6 dpf  rep5", "GSM8553335", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i heterozygous|geo loc name:missing|collection date:missing", "arid1b  6 dpf  rep5", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i heterozygous", "GSM8553335", "GSM8553335: arid1b  6 dpf  rep5; Danio rerio; RNA Seq", "GSM8553335 r1", "GSM8553335", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, null, "arid1b-195d50i-het_AR18_S18_R1_001.fastq.gz", "fastq", 3870464200.0, 38704642.0, "GSM8553335 r1", "0:100", "A:1000259085;C:960215025;G:917241491;T:992680013;N:68586", 100, null, null, null, 1000259085, 960215025, 917241491, 992680013, 68586, "SRX26270358", "SRS22808216", "SRA1985473", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-10-03", "Larval", "Larval", "Multi-tissue", "Multi-system"], [29905, "SRR30873039", "SRX26270357", "SRS22808215", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  6 dpf  rep4", "GSM8553334", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i heterozygous|geo loc name:missing|collection date:missing", "arid1b  6 dpf  rep4", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i heterozygous", "GSM8553334", "GSM8553334: arid1b  6 dpf  rep4; Danio rerio; RNA Seq", "GSM8553334 r1", "GSM8553334", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, null, "arid1b-195d50i-het_AR17_S17_R1_001.fastq.gz", "fastq", 4594184100.0, 45941841.0, "GSM8553334 r1", "0:100", "A:1184283243;C:1151731213;G:1096934508;T:1161152565;N:82571", 100, null, null, null, 1184283243, 1151731213, 1096934508, 1161152565, 82571, "SRX26270357", "SRS22808215", "SRA1985473", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-10-03", "Larval", "Larval", "Multi-tissue", "Multi-system"], [29906, "SRR30873040", "SRX26270356", "SRS22808214", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  6 dpf  rep3", "GSM8553333", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i heterozygous|geo loc name:missing|collection date:missing", "arid1b  6 dpf  rep3", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i heterozygous", "GSM8553333", "GSM8553333: arid1b  6 dpf  rep3; Danio rerio; RNA Seq", "GSM8553333 r1", "GSM8553333", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, null, "arid1b-195d50i-het_AR16_S16_R1_001.fastq.gz", "fastq", 4941522000.0, 49415220.0, "GSM8553333 r1", "0:100", "A:1259383920;C:1247709712;G:1186755788;T:1247582989;N:89591", 100, null, null, null, 1259383920, 1247709712, 1186755788, 1247582989, 89591, "SRX26270356", "SRS22808214", "SRA1985473", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-10-03", "Larval", "Larval", "Multi-tissue", "Multi-system"], [29907, "SRR30873041", "SRX26270355", "SRS22808213", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  6 dpf  rep2", "GSM8553332", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i heterozygous|geo loc name:missing|collection date:missing", "arid1b  6 dpf  rep2", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i heterozygous", "GSM8553332", "GSM8553332: arid1b  6 dpf  rep2; Danio rerio; RNA Seq", "GSM8553332 r1", "GSM8553332", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, null, "arid1b-195d50i-het_AR15_S15_R1_001.fastq.gz", "fastq", 4104651300.0, 41046513.0, "GSM8553332 r1", "0:100", "A:1076649631;C:1007609502;G:973534133;T:1046799245;N:58789", 100, null, null, null, 1076649631, 1007609502, 973534133, 1046799245, 58789, "SRX26270355", "SRS22808213", "SRA1985473", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-10-03", "Larval", "Larval", "Multi-tissue", "Multi-system"], [29908, "SRR30873042", "SRX26270354", "SRS22808212", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  6 dpf  rep1", "GSM8553331", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i heterozygous|geo loc name:missing|collection date:missing", "arid1b  6 dpf  rep1", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:arid1b 195d50i heterozygous", "GSM8553331", "GSM8553331: arid1b  6 dpf  rep1; Danio rerio; RNA Seq", "GSM8553331 r1", "GSM8553331", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, null, "arid1b-195d50i-het_AR14_S14_R1_001.fastq.gz", "fastq", 2182363600.0, 21823636.0, "GSM8553331 r1", "0:100", "A:567445925;C:541275778;G:507884278;T:565718419;N:39200", 100, null, null, null, 567445925, 541275778, 507884278, 565718419, 39200, "SRX26270354", "SRS22808212", "SRA1985473", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-10-03", "Larval", "Larval", "Multi-tissue", "Multi-system"], [29960, "SRR27592985", "SRX23261695", "SRS20163660", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  6 dpf  rep14", "GSM8020155", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing", "deaf1  6 dpf  rep14", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types", "GSM8020155", "GSM8020155: deaf1  6 dpf  rep14; Danio rerio; RNA Seq", "GSM8020155 r1", "GSM8020155", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-6dpf-wt_C4_S28_R1_001.fastq.gz", "fastq", 3929983225.0, 38910725.0, "GSM8020155 r1", "0:101", "A:1024547567;C:957640911;G:915138235;T:1032535260;N:121252", 101, null, null, null, 1024547567, 957640911, 915138235, 1032535260, 121252, "SRX23261695", "SRS20163660", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Larval", "Larval", "Multi-tissue", "Multi-system"]], "truncated": false, "filtered_table_rows_count": 1215, "expanded_columns": [], 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