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We first measured activity following vestibular sensation in pre motor projection neurons post constitutive loss of their extraocular motor neuron partners.We observed normal responses and topography consistent with unchanged functional connectivity between sensory neurons and projection neurons. Next  we show that projection neurons remain anatomically and molecularly poised to connect appropriately with their motor partners. Lastly  we show that the transcriptional signatures of projection neuron subtypes develop independently of motor partners. Our findings comprehensively overturn a long standing model: that connectivity in the circuit for gaze stabilization is retrogradely determined by motor partner derived signals. By defining the contribution of motor neurons to canonical sensorimotor circuit assembly  our work speaks to comparable processes in spinal circuits and advances our understanding of general principles of neural development. 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Our findings comprehensively overturn a long standing model: that connectivity in the circuit for gaze stabilization is retrogradely determined by motor partner derived signals. By defining the contribution of motor neurons to canonical sensorimotor circuit assembly  our work speaks to comparable processes in spinal circuits and advances our understanding of general principles of neural development. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Embyros were from two conditions: larvae from a stable line of phox2a /  mutants  and sibling controls phox2a+/+ or +/ . Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Four experimental repeats were performed  each generating two samples phox2a /  and sibling control. 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Our findings comprehensively overturn a long standing model: that connectivity in the circuit for gaze stabilization is retrogradely determined by motor partner derived signals. By defining the contribution of motor neurons to canonical sensorimotor circuit assembly  our work speaks to comparable processes in spinal circuits and advances our understanding of general principles of neural development. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Embyros were from two conditions: larvae from a stable line of phox2a /  mutants  and sibling controls phox2a+/+ or +/ . Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Four experimental repeats were performed  each generating two samples phox2a /  and sibling control. 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Whether and how motor partner populations shape the subtype fate and connectivity of their pre motor counterparts remains controversial. Here  we discovered that motor partners are dispensable for proper connectivity across an entire vestibular reflex circuit that stabilizes gaze. We first measured activity following vestibular sensation in pre motor projection neurons post constitutive loss of their extraocular motor neuron partners.We observed normal responses and topography consistent with unchanged functional connectivity between sensory neurons and projection neurons. Next  we show that projection neurons remain anatomically and molecularly poised to connect appropriately with their motor partners. Lastly  we show that the transcriptional signatures of projection neuron subtypes develop independently of motor partners. Our findings comprehensively overturn a long standing model: that connectivity in the circuit for gaze stabilization is retrogradely determined by motor partner derived signals. By defining the contribution of motor neurons to canonical sensorimotor circuit assembly  our work speaks to comparable processes in spinal circuits and advances our understanding of general principles of neural development. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Embyros were from two conditions: larvae from a stable line of phox2a /  mutants  and sibling controls phox2a+/+ or +/ . Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Four experimental repeats were performed  each generating two samples phox2a /  and sibling control. 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Whether and how motor partner populations shape the subtype fate and connectivity of their pre motor counterparts remains controversial. Here  we discovered that motor partners are dispensable for proper connectivity across an entire vestibular reflex circuit that stabilizes gaze. We first measured activity following vestibular sensation in pre motor projection neurons post constitutive loss of their extraocular motor neuron partners.We observed normal responses and topography consistent with unchanged functional connectivity between sensory neurons and projection neurons. Next  we show that projection neurons remain anatomically and molecularly poised to connect appropriately with their motor partners. Lastly  we show that the transcriptional signatures of projection neuron subtypes develop independently of motor partners. Our findings comprehensively overturn a long standing model: that connectivity in the circuit for gaze stabilization is retrogradely determined by motor partner derived signals. By defining the contribution of motor neurons to canonical sensorimotor circuit assembly  our work speaks to comparable processes in spinal circuits and advances our understanding of general principles of neural development. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Embyros were from two conditions: larvae from a stable line of phox2a /  mutants  and sibling controls phox2a+/+ or +/ . Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Four experimental repeats were performed  each generating two samples phox2a /  and sibling control. Bulk RNA sequencing was performed.", null, null, null, "Hindbrain vestibular neurons  phox2a /   replicate 2", "GSM8038032", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a / |geo loc name:missing|collection date:missing", "Hindbrain vestibular neurons  phox2a /   replicate 2", "DESeq2 Assembly: GRCz11 Supplementary files format and content: excel file includes raw counts for each sample Supplementary files format and content: excel file includes normalized counts for each sample", "Hindbrain vestibular neurons", null, "RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. 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Whether and how motor partner populations shape the subtype fate and connectivity of their pre motor counterparts remains controversial. Here  we discovered that motor partners are dispensable for proper connectivity across an entire vestibular reflex circuit that stabilizes gaze. We first measured activity following vestibular sensation in pre motor projection neurons post constitutive loss of their extraocular motor neuron partners.We observed normal responses and topography consistent with unchanged functional connectivity between sensory neurons and projection neurons. Next  we show that projection neurons remain anatomically and molecularly poised to connect appropriately with their motor partners. Lastly  we show that the transcriptional signatures of projection neuron subtypes develop independently of motor partners. Our findings comprehensively overturn a long standing model: that connectivity in the circuit for gaze stabilization is retrogradely determined by motor partner derived signals. By defining the contribution of motor neurons to canonical sensorimotor circuit assembly  our work speaks to comparable processes in spinal circuits and advances our understanding of general principles of neural development. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Embyros were from two conditions: larvae from a stable line of phox2a /  mutants  and sibling controls phox2a+/+ or +/ . Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Four experimental repeats were performed  each generating two samples phox2a /  and sibling control. 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Our findings comprehensively overturn a long standing model: that connectivity in the circuit for gaze stabilization is retrogradely determined by motor partner derived signals. By defining the contribution of motor neurons to canonical sensorimotor circuit assembly  our work speaks to comparable processes in spinal circuits and advances our understanding of general principles of neural development. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Embyros were from two conditions: larvae from a stable line of phox2a /  mutants  and sibling controls phox2a+/+ or +/ . Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Four experimental repeats were performed  each generating two samples phox2a /  and sibling control. Bulk RNA sequencing was performed.", null, null, null, "Hindbrain vestibular neurons  phox2a /   replicate 1", "GSM8038030", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a / |geo loc name:missing|collection date:missing", "Hindbrain vestibular neurons  phox2a /   replicate 1", "DESeq2 Assembly: GRCz11 Supplementary files format and content: excel file includes raw counts for each sample Supplementary files format and content: excel file includes normalized counts for each sample", "Hindbrain vestibular neurons", null, "RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a / ", "GSM8038030", "GSM8038030: Hindbrain vestibular neurons  phox2a /   replicate 1; Danio rerio; RNA Seq", "GSM8038030 r1", "GSM8038030", "1", "RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486175", null, "loader:fastq load.py", "1019_phox2a_S25_L002_R1_001.fastq.gz 1019_phox2a_S25_L002_R2_001.fastq.gz", "fastq fastq", 3186783246.0, 31242973.0, "GSM8038030 r1", "0:51 1:51", "A:955687278;C:636490356;G:630374686;T:964170971;N:59955", 51, 51, null, null, 955687278, 636490356, 630374686, 964170971, 59955, "SRX23412762", "SRS20268083", "SRA1792521", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-26", "Larval", "Larval", "Brain", "Nervous System"], [30283, "SRR27747459", "SRX23412761", "SRS20268082", "SRP486175", "PRJNA1069777", "Effect of phox2a knockout on the molecular profiles of hindbrain vestibular neurons in the larval zebrafish bulk RNA Seq", "GSE254345", "Transcriptome Analysis", "Sensorimotor reflex circuits engage distinct neuronal subtypes  defined by precise connectivity  to transform sensation into compensatory behavior. Whether and how motor partner populations shape the subtype fate and connectivity of their pre motor counterparts remains controversial. Here  we discovered that motor partners are dispensable for proper connectivity across an entire vestibular reflex circuit that stabilizes gaze. We first measured activity following vestibular sensation in pre motor projection neurons post constitutive loss of their extraocular motor neuron partners.We observed normal responses and topography consistent with unchanged functional connectivity between sensory neurons and projection neurons. Next  we show that projection neurons remain anatomically and molecularly poised to connect appropriately with their motor partners. Lastly  we show that the transcriptional signatures of projection neuron subtypes develop independently of motor partners. Our findings comprehensively overturn a long standing model: that connectivity in the circuit for gaze stabilization is retrogradely determined by motor partner derived signals. By defining the contribution of motor neurons to canonical sensorimotor circuit assembly  our work speaks to comparable processes in spinal circuits and advances our understanding of general principles of neural development. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Embyros were from two conditions: larvae from a stable line of phox2a /  mutants  and sibling controls phox2a+/+ or +/ . Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Four experimental repeats were performed  each generating two samples phox2a /  and sibling control. Bulk RNA sequencing was performed.", null, null, null, "Hindbrain vestibular neurons  siblings  replicate 1", "GSM8038029", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a+/+ or +/ |geo loc name:missing|collection date:missing", "Hindbrain vestibular neurons  siblings  replicate 1", "DESeq2 Assembly: GRCz11 Supplementary files format and content: excel file includes raw counts for each sample Supplementary files format and content: excel file includes normalized counts for each sample", "Hindbrain vestibular neurons", null, "RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede; Tgisl1:GFP; phox2a+/+ or +/ ", "GSM8038029", "GSM8038029: Hindbrain vestibular neurons  siblings  replicate 1; Danio rerio; RNA Seq", "GSM8038029 r1", "GSM8038029", "1", "RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system. Libraries for bulk RNA sequencing were prepared using the low input Clontech SMART Seq HT with Nxt HT kit Takara", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486175", null, "loader:fastq load.py", "1019_siblings_S26_L002_R1_001.fastq.gz 1019_siblings_S26_L002_R2_001.fastq.gz", "fastq fastq", 3481817226.0, 34135463.0, "GSM8038029 r1", "0:51 1:51", "A:1015152374;C:724318215;G:717469149;T:1024812342;N:65146", 51, 51, null, null, 1015152374, 724318215, 717469149, 1024812342, 65146, "SRX23412761", "SRS20268082", "SRA1792521", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-26", "Larval", "Larval", "Brain", "Nervous System"], [33311, "SRR29927545", "SRX25421505", "SRS22081661", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "ON 3d rep3", "MCWR 2019 000157", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:female|tissue:optic nerve|treatment:ON 3d rep3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 3 xxx post injury optic nerve", "ON 3d rep3", "ON 3d rep3", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000157_S28_L001_R1_001.fastq.gz MCWR_2019_000157_S28_L001_R2_001.fastq.gz MCWR_2019_000157_S28_L002_R1_001.fastq.gz MCWR_2019_000157_S28_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 12637756180.0, 41976869.0, "MCWR 2019 000157 S28 L001 R1 001.fastq.gz", "0:150.53 1:150.53", "A:3303913534;C:3007130754;G:3036624621;T:3289934437;N:152834", 150, 150, null, null, 3303913534, 3007130754, 3036624621, 3289934437, 152834, "SRX25421505", "SRS22081661", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.9516, 0.95161, 0.06268, 0.06324, 0.7245, 0.72539, 0.50499, 0.5082, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Brain", "Nervous System"], [33312, "SRR29927546", "SRX25421504", "SRS22081660", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "ON 3d rep2", "MCWR 2019 000156", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:female|tissue:optic nerve|treatment:ON 3d rep2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 3 xxx post injury optic nerve", "ON 3d rep2", "ON 3d rep2", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000156_S27_L001_R1_001.fastq.gz MCWR_2019_000156_S27_L001_R2_001.fastq.gz MCWR_2019_000156_S27_L002_R1_001.fastq.gz MCWR_2019_000156_S27_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 8225156065.0, 27320970.0, "MCWR 2019 000156 S27 L001 R1 001.fastq.gz", "0:150.53 1:150.53", "A:2177338510;C:1933476228;G:1950713017;T:2163526872;N:101438", 150, 150, null, null, 2177338510, 1933476228, 1950713017, 2163526872, 101438, "SRX25421504", "SRS22081660", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.94816, 0.94656, 0.06839, 0.06869, 0.71873, 0.72099, 0.52048, 0.51823, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Brain", "Nervous System"], [33314, "SRR29927548", "SRX25421502", "SRS22081658", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "ON 3d rep1", "MCWR 2019 000149", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:female|tissue:optic nerve|treatment:ON 3d rep1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 3 xxx post injury optic nerve", "ON 3d rep1", "ON 3d rep1", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000149_S20_L001_R1_001.fastq.gz MCWR_2019_000149_S20_L001_R2_001.fastq.gz MCWR_2019_000149_S20_L002_R1_001.fastq.gz MCWR_2019_000149_S20_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 11234251579.0, 37312508.0, "MCWR 2019 000149 S20 L001 R1 001.fastq.gz", "0:150.54 1:150.55", "A:2884045359;C:2724366727;G:2744442031;T:2881252209;N:145253", 150, 150, null, null, 2884045359, 2724366727, 2744442031, 2881252209, 145253, "SRX25421502", "SRS22081658", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.95118, 0.95151, 0.09345, 0.09458, 0.69589, 0.6953, 0.47864, 0.4794, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Brain", "Nervous System"], [33315, "SRR29927549", "SRX25421501", "SRS22081657", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "ON Control rep3", "MCWR 2019 000148", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:female|tissue:optic nerve|treatment:ON Control rep3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: naive optic nerve", "ON Control rep3", "ON Control rep3", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000148_S19_L002_R2_001.fastq.gz MCWR_2019_000148_S19_L002_R1_001.fastq.gz MCWR_2019_000148_S19_L001_R2_001.fastq.gz MCWR_2019_000148_S19_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 10659326860.0, 35402192.0, "MCWR 2019 000148 S19 L001 R1 001.fastq.gz", "0:150.55 1:150.55", "A:2756153864;C:2571019186;G:2591020090;T:2740998974;N:134746", 150, 150, null, null, 2756153864, 2571019186, 2591020090, 2740998974, 134746, "SRX25421501", "SRS22081657", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.95167, 0.95091, 0.09159, 0.09247, 0.74852, 0.74961, 0.46451, 0.46354, 150, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Brain", "Nervous System"], [33316, "SRR29927550", "SRX25421500", "SRS22081656", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "ON Control rep2", "MCWR 2019 000147", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:female|tissue:optic nerve|treatment:ON Control rep2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: naive optic nerve", "ON Control rep2", "ON Control rep2", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000147_S18_L002_R2_001.fastq.gz MCWR_2019_000147_S18_L002_R1_001.fastq.gz MCWR_2019_000147_S18_L001_R2_001.fastq.gz MCWR_2019_000147_S18_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 13568087444.0, 45061061.0, "MCWR 2019 000147 S18 L001 R1 001.fastq.gz", "0:150.55 1:150.55", "A:3431511167;C:3343690230;G:3365044224;T:3427668362;N:173461", 150, 150, null, null, 3431511167, 3343690230, 3365044224, 3427668362, 173461, "SRX25421500", "SRS22081656", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.95653, 0.95547, 0.08512, 0.08497, 0.73093, 0.73143, 0.46625, 0.46899, 150, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Brain", "Nervous System"], [33317, "SRR29927551", "SRX25421499", "SRS22081655", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues  we performed laser capture mRNA sequencing of the retinal ganglion cell layer  inner nuclear layer  outer nuclear layer  and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "ON Control rep1", "MCWR 2019 000146", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin  Milwaukee|sex:female|tissue:optic nerve|treatment:ON Control rep1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: naive optic nerve", "ON Control rep1", "ON Control rep1", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000146_S17_L002_R2_001.fastq.gz MCWR_2019_000146_S17_L002_R1_001.fastq.gz MCWR_2019_000146_S17_L001_R2_001.fastq.gz MCWR_2019_000146_S17_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 10264964293.0, 34089023.0, "MCWR 2019 000146 S17 L001 R1 001.fastq.gz", "0:150.56 1:150.56", "A:2551033720;C:2573448189;G:2588121299;T:2552234053;N:127032", 150, 150, null, null, 2551033720, 2573448189, 2588121299, 2552234053, 127032, "SRX25421499", "SRS22081655", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.95724, 0.95715, 0.07005, 0.07059, 0.75637, 0.75732, 0.42392, 0.41384, 151, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Brain", "Nervous System"], [34925, "SRR32424865", "SRX27754020", "SRS24139551", "SRP565442", "PRJNA1226487", "Separate brainstem circuits for fast steering and slow exploratory turns", "GSE290157", "Transcriptome Analysis", "During locomotion  trajectory changes necessitate precise tuning of descending commands to scale turning movements according to specific tasks or objectives  resulting in either rapid steering turns during prey pursuit or routine shallow turns associated with exploration. We show that these two types of turning are controlled by separate brainstem circuits that encode rapid steering turning versus slow exploratory turns. The circuit for rapid steering is widely distributed across different brainstem nuclei  involving specific excitatory V2a and inhibitory commissural V0d neurons. The steering V2a and V0d neurons are furthermore coupled via gap junctions and simultaneously recruited to ensure rapid steering through an asymmetrical recruitment of spinal motor neurons. The recruitment of these steering neurons is primarily associated with the degree of the direction change  rather than the locomotor frequency. The brainstem steering neurons are  in turn  controlled by a subset of V2a neurons in the pretectum activated by salient visual input. Conversely  the circuit controlling swim related slow exploratory turns comprises a different set of V2a neurons localized in fewer brainstem nuclei. These findings demonstrate a modular organization of the brainstem circuits that control rapid steering and slow exploratory turning during locomotion. Overall design: CaD neurons were taken fromTg  gly2: GFP zebrafish brain stem  one cell from each fish  a total of eight fish", null, null, null, "Glycinergic neurons m17", "GSM8807155", null, "tissue:Glycinergic neurons|cell type:Glycinergic neurons|genotype:Tg gly2: GFP|geo loc name:missing|collection date:missing", "Glycinergic neurons m17", "Raw data raw reads of fastq format were firstly processed through in house perl scripts.In this step  clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non splice mapping tools. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Assembly: danio rerio Ensembl 97 Supplementary files format and content: FPKM values for each samples.", "Glycinergic neurons", null, "RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA  Inc. Sequencing libraries were generated using NEBNext\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample.", null, "cell type:Glycinergic neurons|genotype:Tg gly2: GFP", "GSM8807155", "GSM8807155: Glycinergic neurons m17; Danio rerio; RNA Seq", "GSM8807155 r1", "GSM8807155", "1", "RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA  Inc. Sequencing libraries were generated using NEBNext\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP565442", null, null, "M17_1.fq.gz M17_2.fq.gz", "fastq fastq", 7922316510.0, 28870507.0, "GSM8807155 r1", null, "A:2259269798;C:1309791881;G:1358854827;T:2993890708;N:509296", null, null, null, null, 2259269798, 1309791881, 1358854827, 2993890708, 509296, "SRX27754020", "SRS24139551", "SRA2081247", "TongJi university", "TongJi university", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2025-02-21", "Undetermined", "Undetermined", "Brain", "Nervous System"], [34926, "SRR32424866", "SRX27754019", "SRS24139550", "SRP565442", "PRJNA1226487", "Separate brainstem circuits for fast steering and slow exploratory turns", "GSE290157", "Transcriptome Analysis", "During locomotion  trajectory changes necessitate precise tuning of descending commands to scale turning movements according to specific tasks or objectives  resulting in either rapid steering turns during prey pursuit or routine shallow turns associated with exploration. We show that these two types of turning are controlled by separate brainstem circuits that encode rapid steering turning versus slow exploratory turns. The circuit for rapid steering is widely distributed across different brainstem nuclei  involving specific excitatory V2a and inhibitory commissural V0d neurons. The steering V2a and V0d neurons are furthermore coupled via gap junctions and simultaneously recruited to ensure rapid steering through an asymmetrical recruitment of spinal motor neurons. The recruitment of these steering neurons is primarily associated with the degree of the direction change  rather than the locomotor frequency. The brainstem steering neurons are  in turn  controlled by a subset of V2a neurons in the pretectum activated by salient visual input. Conversely  the circuit controlling swim related slow exploratory turns comprises a different set of V2a neurons localized in fewer brainstem nuclei. These findings demonstrate a modular organization of the brainstem circuits that control rapid steering and slow exploratory turning during locomotion. Overall design: CaD neurons were taken fromTg  gly2: GFP zebrafish brain stem  one cell from each fish  a total of eight fish", null, null, null, "Glycinergic neurons m16", "GSM8807154", null, "tissue:Glycinergic neurons|cell type:Glycinergic neurons|genotype:Tg gly2: GFP|geo loc name:missing|collection date:missing", "Glycinergic neurons m16", "Raw data raw reads of fastq format were firstly processed through in house perl scripts.In this step  clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non splice mapping tools. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Assembly: danio rerio Ensembl 97 Supplementary files format and content: FPKM values for each samples.", "Glycinergic neurons", null, "RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA  Inc. Sequencing libraries were generated using NEBNext\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample.", null, "cell type:Glycinergic neurons|genotype:Tg gly2: GFP", "GSM8807154", "GSM8807154: Glycinergic neurons m16; Danio rerio; RNA Seq", "GSM8807154 r1", "GSM8807154", "1", "RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA  Inc. Sequencing libraries were generated using NEBNext\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP565442", null, null, "M16_1.fq.gz M16_2.fq.gz", "fastq fastq", 7720739055.0, 27919217.0, "GSM8807154 r1", null, "A:2250075980;C:1271393485;G:1306175216;T:2892579232;N:515142", null, null, null, null, 2250075980, 1271393485, 1306175216, 2892579232, 515142, "SRX27754019", "SRS24139550", "SRA2081247", "TongJi university", "TongJi university", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2025-02-21", "Undetermined", "Undetermined", "Brain", "Nervous System"], [34927, "SRR32424867", "SRX27754018", "SRS24139549", "SRP565442", "PRJNA1226487", "Separate brainstem circuits for fast steering and slow exploratory turns", "GSE290157", "Transcriptome Analysis", "During locomotion  trajectory changes necessitate precise tuning of descending commands to scale turning movements according to specific tasks or objectives  resulting in either rapid steering turns during prey pursuit or routine shallow turns associated with exploration. We show that these two types of turning are controlled by separate brainstem circuits that encode rapid steering turning versus slow exploratory turns. The circuit for rapid steering is widely distributed across different brainstem nuclei  involving specific excitatory V2a and inhibitory commissural V0d neurons. The steering V2a and V0d neurons are furthermore coupled via gap junctions and simultaneously recruited to ensure rapid steering through an asymmetrical recruitment of spinal motor neurons. The recruitment of these steering neurons is primarily associated with the degree of the direction change  rather than the locomotor frequency. The brainstem steering neurons are  in turn  controlled by a subset of V2a neurons in the pretectum activated by salient visual input. Conversely  the circuit controlling swim related slow exploratory turns comprises a different set of V2a neurons localized in fewer brainstem nuclei. These findings demonstrate a modular organization of the brainstem circuits that control rapid steering and slow exploratory turning during locomotion. Overall design: CaD neurons were taken fromTg  gly2: GFP zebrafish brain stem  one cell from each fish  a total of eight fish", null, null, null, "Glycinergic neurons m11", "GSM8807153", null, "tissue:Glycinergic neurons|cell type:Glycinergic neurons|genotype:Tg gly2: GFP|geo loc name:missing|collection date:missing", "Glycinergic neurons m11", "Raw data raw reads of fastq format were firstly processed through in house perl scripts.In this step  clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non splice mapping tools. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Assembly: danio rerio Ensembl 97 Supplementary files format and content: FPKM values for each samples.", "Glycinergic neurons", null, "RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA  Inc. Sequencing libraries were generated using NEBNext\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample.", null, "cell type:Glycinergic neurons|genotype:Tg gly2: GFP", "GSM8807153", "GSM8807153: Glycinergic neurons m11; Danio rerio; RNA Seq", "GSM8807153 r1", "GSM8807153", "1", "RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA  Inc. Sequencing libraries were generated using NEBNext\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP565442", null, null, "M11_1.fq.gz M11_2.fq.gz", "fastq fastq", 6830992776.0, 24127264.0, "GSM8807153 r1", null, "A:1949282464;C:1265666713;G:1276892181;T:2338677805;N:473613", null, null, null, null, 1949282464, 1265666713, 1276892181, 2338677805, 473613, "SRX27754018", "SRS24139549", "SRA2081247", "TongJi university", "TongJi university", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2025-02-21", "Undetermined", "Undetermined", "Brain", "Nervous System"], [34928, "SRR32424868", "SRX27754017", "SRS24139548", "SRP565442", "PRJNA1226487", "Separate brainstem circuits for fast steering and slow exploratory turns", "GSE290157", "Transcriptome Analysis", "During locomotion  trajectory changes necessitate precise tuning of descending commands to scale turning movements according to specific tasks or objectives  resulting in either rapid steering turns during prey pursuit or routine shallow turns associated with exploration. We show that these two types of turning are controlled by separate brainstem circuits that encode rapid steering turning versus slow exploratory turns. The circuit for rapid steering is widely distributed across different brainstem nuclei  involving specific excitatory V2a and inhibitory commissural V0d neurons. The steering V2a and V0d neurons are furthermore coupled via gap junctions and simultaneously recruited to ensure rapid steering through an asymmetrical recruitment of spinal motor neurons. The recruitment of these steering neurons is primarily associated with the degree of the direction change  rather than the locomotor frequency. The brainstem steering neurons are  in turn  controlled by a subset of V2a neurons in the pretectum activated by salient visual input. Conversely  the circuit controlling swim related slow exploratory turns comprises a different set of V2a neurons localized in fewer brainstem nuclei. These findings demonstrate a modular organization of the brainstem circuits that control rapid steering and slow exploratory turning during locomotion. Overall design: CaD neurons were taken fromTg  gly2: GFP zebrafish brain stem  one cell from each fish  a total of eight fish", null, null, null, "Glycinergic neurons m9", "GSM8807152", null, "tissue:Glycinergic neurons|cell type:Glycinergic neurons|genotype:Tg gly2: GFP|geo loc name:missing|collection date:missing", "Glycinergic neurons m9", "Raw data raw reads of fastq format were firstly processed through in house perl scripts.In this step  clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non splice mapping tools. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Assembly: danio rerio Ensembl 97 Supplementary files format and content: FPKM values for each samples.", "Glycinergic neurons", null, "RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA  Inc. Sequencing libraries were generated using NEBNext\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample.", null, "cell type:Glycinergic neurons|genotype:Tg gly2: GFP", "GSM8807152", "GSM8807152: Glycinergic neurons m9; Danio rerio; RNA Seq", "GSM8807152 r1", "GSM8807152", "1", "RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA  Inc. Sequencing libraries were generated using NEBNext\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP565442", null, null, "M9_1.fq.gz M9_2.fq.gz", "fastq fastq", 7582940148.0, 27320994.0, "GSM8807152 r1", null, "A:2107584201;C:1339317674;G:1381218723;T:2754261953;N:557597", null, null, null, null, 2107584201, 1339317674, 1381218723, 2754261953, 557597, "SRX27754017", "SRS24139548", "SRA2081247", "TongJi university", "TongJi university", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2025-02-21", "Undetermined", "Undetermined", "Brain", "Nervous System"], [34929, "SRR32424869", "SRX27754016", "SRS24139547", "SRP565442", "PRJNA1226487", "Separate brainstem circuits for fast steering and slow exploratory turns", "GSE290157", "Transcriptome Analysis", "During locomotion  trajectory changes necessitate precise tuning of descending commands to scale turning movements according to specific tasks or objectives  resulting in either rapid steering turns during prey pursuit or routine shallow turns associated with exploration. We show that these two types of turning are controlled by separate brainstem circuits that encode rapid steering turning versus slow exploratory turns. The circuit for rapid steering is widely distributed across different brainstem nuclei  involving specific excitatory V2a and inhibitory commissural V0d neurons. The steering V2a and V0d neurons are furthermore coupled via gap junctions and simultaneously recruited to ensure rapid steering through an asymmetrical recruitment of spinal motor neurons. The recruitment of these steering neurons is primarily associated with the degree of the direction change  rather than the locomotor frequency. The brainstem steering neurons are  in turn  controlled by a subset of V2a neurons in the pretectum activated by salient visual input. Conversely  the circuit controlling swim related slow exploratory turns comprises a different set of V2a neurons localized in fewer brainstem nuclei. These findings demonstrate a modular organization of the brainstem circuits that control rapid steering and slow exploratory turning during locomotion. Overall design: CaD neurons were taken fromTg  gly2: GFP zebrafish brain stem  one cell from each fish  a total of eight fish", null, null, null, "Glycinergic neurons m6", "GSM8807151", null, "tissue:Glycinergic neurons|cell type:Glycinergic neurons|genotype:Tg gly2: GFP|geo loc name:missing|collection date:missing", "Glycinergic neurons m6", "Raw data raw reads of fastq format were firstly processed through in house perl scripts.In this step  clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non splice mapping tools. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Assembly: danio rerio Ensembl 97 Supplementary files format and content: FPKM values for each samples.", "Glycinergic neurons", null, "RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA  Inc. Sequencing libraries were generated using NEBNext\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample.", null, "cell type:Glycinergic neurons|genotype:Tg gly2: GFP", "GSM8807151", "GSM8807151: Glycinergic neurons m6; Danio rerio; RNA Seq", "GSM8807151 r1", "GSM8807151", "1", "RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA  Inc. Sequencing libraries were generated using NEBNext\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP565442", null, null, "M6_1.fq.gz M6_2.fq.gz", "fastq fastq", 7719009952.0, 27333519.0, "GSM8807151 r1", null, "A:2131513261;C:1443134919;G:1469022783;T:2672576370;N:2762619", null, null, null, null, 2131513261, 1443134919, 1469022783, 2672576370, 2762619, "SRX27754016", "SRS24139547", "SRA2081247", "TongJi university", "TongJi university", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2025-02-21", "Undetermined", "Undetermined", "Brain", "Nervous System"], [34930, "SRR32424870", "SRX27754015", "SRS24139546", "SRP565442", "PRJNA1226487", "Separate brainstem circuits for fast steering and slow exploratory turns", "GSE290157", "Transcriptome Analysis", "During locomotion  trajectory changes necessitate precise tuning of descending commands to scale turning movements according to specific tasks or objectives  resulting in either rapid steering turns during prey pursuit or routine shallow turns associated with exploration. We show that these two types of turning are controlled by separate brainstem circuits that encode rapid steering turning versus slow exploratory turns. The circuit for rapid steering is widely distributed across different brainstem nuclei  involving specific excitatory V2a and inhibitory commissural V0d neurons. The steering V2a and V0d neurons are furthermore coupled via gap junctions and simultaneously recruited to ensure rapid steering through an asymmetrical recruitment of spinal motor neurons. The recruitment of these steering neurons is primarily associated with the degree of the direction change  rather than the locomotor frequency. The brainstem steering neurons are  in turn  controlled by a subset of V2a neurons in the pretectum activated by salient visual input. Conversely  the circuit controlling swim related slow exploratory turns comprises a different set of V2a neurons localized in fewer brainstem nuclei. These findings demonstrate a modular organization of the brainstem circuits that control rapid steering and slow exploratory turning during locomotion. Overall design: CaD neurons were taken fromTg  gly2: GFP zebrafish brain stem  one cell from each fish  a total of eight fish", null, null, null, "Glycinergic neurons m5", "GSM8807150", null, "tissue:Glycinergic neurons|cell type:Glycinergic neurons|genotype:Tg gly2: GFP|geo loc name:missing|collection date:missing", "Glycinergic neurons m5", "Raw data raw reads of fastq format were firstly processed through in house perl scripts.In this step  clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non splice mapping tools. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Assembly: danio rerio Ensembl 97 Supplementary files format and content: FPKM values for each samples.", "Glycinergic neurons", null, "RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA  Inc. Sequencing libraries were generated using NEBNext\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample.", null, "cell type:Glycinergic neurons|genotype:Tg gly2: GFP", "GSM8807150", "GSM8807150: Glycinergic neurons m5; Danio rerio; RNA Seq", "GSM8807150 r1", "GSM8807150", "1", "RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA  Inc. Sequencing libraries were generated using NEBNext\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP565442", null, null, "M5_1.fq.gz M5_2.fq.gz", "fastq fastq", 8381104622.0, 30664708.0, "GSM8807150 r1", null, "A:2289409726;C:1427540731;G:1492945660;T:3168884923;N:2323582", null, null, null, null, 2289409726, 1427540731, 1492945660, 3168884923, 2323582, "SRX27754015", "SRS24139546", "SRA2081247", "TongJi university", "TongJi university", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2025-02-21", "Undetermined", "Undetermined", "Brain", "Nervous System"], [34931, "SRR32424871", "SRX27754014", "SRS24139545", "SRP565442", "PRJNA1226487", "Separate brainstem circuits for fast steering and slow exploratory turns", "GSE290157", "Transcriptome Analysis", "During locomotion  trajectory changes necessitate precise tuning of descending commands to scale turning movements according to specific tasks or objectives  resulting in either rapid steering turns during prey pursuit or routine shallow turns associated with exploration. We show that these two types of turning are controlled by separate brainstem circuits that encode rapid steering turning versus slow exploratory turns. The circuit for rapid steering is widely distributed across different brainstem nuclei  involving specific excitatory V2a and inhibitory commissural V0d neurons. The steering V2a and V0d neurons are furthermore coupled via gap junctions and simultaneously recruited to ensure rapid steering through an asymmetrical recruitment of spinal motor neurons. The recruitment of these steering neurons is primarily associated with the degree of the direction change  rather than the locomotor frequency. The brainstem steering neurons are  in turn  controlled by a subset of V2a neurons in the pretectum activated by salient visual input. Conversely  the circuit controlling swim related slow exploratory turns comprises a different set of V2a neurons localized in fewer brainstem nuclei. These findings demonstrate a modular organization of the brainstem circuits that control rapid steering and slow exploratory turning during locomotion. Overall design: CaD neurons were taken fromTg  gly2: GFP zebrafish brain stem  one cell from each fish  a total of eight fish", null, null, null, "Glycinergic neurons m2", "GSM8807149", null, "tissue:Glycinergic neurons|cell type:Glycinergic neurons|genotype:Tg gly2: GFP|geo loc name:missing|collection date:missing", "Glycinergic neurons m2", "Raw data raw reads of fastq format were firstly processed through in house perl scripts.In this step  clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non splice mapping tools. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Assembly: danio rerio Ensembl 97 Supplementary files format and content: FPKM values for each samples.", "Glycinergic neurons", null, "RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA  Inc. Sequencing libraries were generated using NEBNext\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample.", null, "cell type:Glycinergic neurons|genotype:Tg gly2: GFP", "GSM8807149", "GSM8807149: Glycinergic neurons m2; Danio rerio; RNA Seq", "GSM8807149 r1", "GSM8807149", "1", "RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA  Inc. Sequencing libraries were generated using NEBNext\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP565442", null, null, "M2_1.fq.gz M2_2.fq.gz", "fastq fastq", 8672887150.0, 31410837.0, "GSM8807149 r1", null, "A:2358621884;C:1534269208;G:1583773576;T:3192613040;N:3609442", null, null, null, null, 2358621884, 1534269208, 1583773576, 3192613040, 3609442, "SRX27754014", "SRS24139545", "SRA2081247", "TongJi university", "TongJi university", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2025-02-21", "Undetermined", "Undetermined", "Brain", "Nervous System"], [34932, "SRR32424872", "SRX27754013", "SRS24139544", "SRP565442", "PRJNA1226487", "Separate brainstem circuits for fast steering and slow exploratory turns", "GSE290157", "Transcriptome Analysis", "During locomotion  trajectory changes necessitate precise tuning of descending commands to scale turning movements according to specific tasks or objectives  resulting in either rapid steering turns during prey pursuit or routine shallow turns associated with exploration. We show that these two types of turning are controlled by separate brainstem circuits that encode rapid steering turning versus slow exploratory turns. The circuit for rapid steering is widely distributed across different brainstem nuclei  involving specific excitatory V2a and inhibitory commissural V0d neurons. The steering V2a and V0d neurons are furthermore coupled via gap junctions and simultaneously recruited to ensure rapid steering through an asymmetrical recruitment of spinal motor neurons. The recruitment of these steering neurons is primarily associated with the degree of the direction change  rather than the locomotor frequency. The brainstem steering neurons are  in turn  controlled by a subset of V2a neurons in the pretectum activated by salient visual input. Conversely  the circuit controlling swim related slow exploratory turns comprises a different set of V2a neurons localized in fewer brainstem nuclei. These findings demonstrate a modular organization of the brainstem circuits that control rapid steering and slow exploratory turning during locomotion. Overall design: CaD neurons were taken fromTg  gly2: GFP zebrafish brain stem  one cell from each fish  a total of eight fish", null, null, null, "Glycinergic neurons m1", "GSM8807148", null, "tissue:Glycinergic neurons|cell type:Glycinergic neurons|genotype:Tg gly2: GFP|geo loc name:missing|collection date:missing", "Glycinergic neurons m1", "Raw data raw reads of fastq format were firstly processed through in house perl scripts.In this step  clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non splice mapping tools. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Assembly: danio rerio Ensembl 97 Supplementary files format and content: FPKM values for each samples.", "Glycinergic neurons", null, "RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA  Inc. Sequencing libraries were generated using NEBNext\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample.", null, "cell type:Glycinergic neurons|genotype:Tg gly2: GFP", "GSM8807148", "GSM8807148: Glycinergic neurons m1; Danio rerio; RNA Seq", "GSM8807148 r1", "GSM8807148", "1", "RNA was harvested using SMART Seq v4 Ultra Low Input RNA Kit Takara Bio USA  Inc. Sequencing libraries were generated using NEBNext\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP565442", null, null, "M1_1.fq.gz M1_2.fq.gz", "fastq fastq", 30591542380.0, 110161442.0, "GSM8807148 r1", null, "A:8730028799;C:5294263499;G:5420191319;T:11143275950;N:3782813", null, null, null, null, 8730028799, 5294263499, 5420191319, 11143275950, 3782813, "SRX27754013", "SRS24139544", "SRA2081247", "TongJi university", "TongJi university", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2025-02-21", "Undetermined", "Undetermined", "Brain", "Nervous System"], [40482, "SRR3183446", "SRX1597282", "SRS1307292", "SRP070686", "PRJNA312899", "Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction", "GSE78194", "Transcriptome Analysis", "transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control   upon macrophage arrival   and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.", null, "pubmed:27156384", null, "mac repair2", "GSM2069441", null, "source name:mac repair|strain:ABGO|fluorescence:Kaedared|lesion stg:macrophage traction|tissue:brain|cell type:Macrophage", "mac repair2", "Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software  and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and |log2 ratio|\u22651 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology  http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes  http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type", "mac repair", null, "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", null, "strain:ABGO|fluorescence:Kaedared|lesion stg:macrophage traction|tissue:brain|cell type:Macrophage", "GSM2069441", "GSM2069441: mac repair2; Danio rerio; RNA Seq", "GSM2069441", null, "1", "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", "GEO Accession:GSM2069441", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP070686", null, null, "mac-repair4-SC038_1.fq.gz mac-repair4-SC038_2.fq.gz", "fastq fastq", 5301635532.0, 26540791.0, "GSM2069441 r1", "0:99.88 1:99.88", "A:1455876159;C:1213611469;G:1209697136;T:1422373935;N:76833", 99, 99, null, null, 1455876159, 1213611469, 1209697136, 1422373935, 76833, "SRX1597282", "SRS1307292", "SRA356990", "GEO", "SouthWest university Of China", 2, 0.90904, 0.90891, 0.13484, 0.13454, 0.75566, 0.75517, 0.54043, 0.5377, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2016-02-23", "Larval", "Larval", "Brain", "Nervous System"], [40483, "SRR3183445", "SRX1597281", "SRS1307293", "SRP070686", "PRJNA312899", "Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction", "GSE78194", "Transcriptome Analysis", "transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control   upon macrophage arrival   and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.", null, "pubmed:27156384", null, "mac con2", "GSM2069440", null, "source name:mac con|strain:ABGO|fluorescence:Kaedared|lesion stg:uninjured control|tissue:brain|cell type:Macrophage", "mac con2", "Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software  and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and |log2 ratio|\u22651 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology  http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes  http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type", "mac con", null, "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", null, "strain:ABGO|fluorescence:Kaedared|lesion stg:uninjured control|tissue:brain|cell type:Macrophage", "GSM2069440", "GSM2069440: mac con2; Danio rerio; RNA Seq", "GSM2069440", null, "1", "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", "GEO Accession:GSM2069440", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP070686", null, null, "mac-con2-SC019_2.fq.gz mac-con2-SC019_1.fq.gz", "fastq fastq", 6320110276.0, 31638738.0, "GSM2069440 r1", "0:99.88 1:99.88", "A:1939242414;C:1232507136;G:1227176155;T:1921089930;N:94641", 99, 99, null, null, 1939242414, 1232507136, 1227176155, 1921089930, 94641, "SRX1597281", "SRS1307293", "SRA356990", "GEO", "SouthWest university Of China", 2, 0.83136, 0.8313, 0.58017, 0.58041, 0.86628, 0.86669, 0.59968, 0.59677, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2016-02-23", "Larval", "Larval", "Brain", "Nervous System"], [40484, "SRR3183444", "SRX1597280", "SRS1307294", "SRP070686", "PRJNA312899", "Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction", "GSE78194", "Transcriptome Analysis", "transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control   upon macrophage arrival   and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.", null, "pubmed:27156384", null, "mac ab2", "GSM2069439", null, "source name:mac ab|strain:ABGO|fluorescence:Kaedared|lesion stg:macrophage arrival|tissue:brain|cell type:Macrophage", "mac ab2", "Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software  and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and |log2 ratio|\u22651 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology  http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes  http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type", "mac ab", null, "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", null, "strain:ABGO|fluorescence:Kaedared|lesion stg:macrophage arrival|tissue:brain|cell type:Macrophage", "GSM2069439", "GSM2069439: mac ab2; Danio rerio; RNA Seq", "GSM2069439", null, "1", "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", "GEO Accession:GSM2069439", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP070686", null, null, "mac-ab3-SC035_1.fq.gz mac-ab3-SC035_2.fq.gz", "fastq fastq", 6565165025.0, 32864923.0, "GSM2069439 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX1597280", "SRS1307294", "SRA356990", "GEO", "SouthWest university Of China", 2, 0.93107, 0.92872, 0.26305, 0.26195, 0.82686, 0.82712, 0.54026, 0.54, 100, 98, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2016-02-23", "Larval", "Larval", "Brain", "Nervous System"], [40485, "SRR3183443", "SRX1597279", "SRS1307295", "SRP070686", "PRJNA312899", "Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction", "GSE78194", "Transcriptome Analysis", "transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control   upon macrophage arrival   and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.", null, "pubmed:27156384", null, "EC repair2", "GSM2069438", null, "source name:EC repair|strain:ABGO|fluorescence:Dendra2red|lesion stg:macrophage traction|tissue:brain|cell type:Endothelial cell", "EC repair2", "Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software  and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and |log2 ratio|\u22651 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology  http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes  http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type", "EC repair", null, "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", null, "strain:ABGO|fluorescence:Dendra2red|lesion stg:macrophage traction|tissue:brain|cell type:Endothelial cell", "GSM2069438", "GSM2069438: EC repair2; Danio rerio; RNA Seq", "GSM2069438", null, "1", "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", "GEO Accession:GSM2069438", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP070686", null, null, "EC-repair2-SC028_1.fq.gz EC-repair2-SC028_2.fq.gz", "fastq fastq", 5464573374.0, 27356971.0, "GSM2069438 r1", "0:99.88 1:99.88", "A:1574953192;C:1193040049;G:1183625694;T:1512874939;N:79500", 99, 99, null, null, 1574953192, 1193040049, 1183625694, 1512874939, 79500, "SRX1597279", "SRS1307295", "SRA356990", "GEO", "SouthWest university Of China", 2, 0.89166, 0.8896, 0.27558, 0.27603, 0.87278, 0.87221, 0.60926, 0.60627, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2016-02-23", "Larval", "Larval", "Brain", "Nervous System"], [40486, "SRR3183442", "SRX1597278", "SRS1307296", "SRP070686", "PRJNA312899", "Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction", "GSE78194", "Transcriptome Analysis", "transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control   upon macrophage arrival   and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.", null, "pubmed:27156384", null, "EC con2", "GSM2069437", null, "source name:EC con|strain:ABGO|fluorescence:Dendra2red|lesion stg:uninjured control|tissue:brain|cell type:Endothelial cell", "EC con2", "Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software  and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and |log2 ratio|\u22651 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology  http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes  http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type", "EC con", null, "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", null, "strain:ABGO|fluorescence:Dendra2red|lesion stg:uninjured control|tissue:brain|cell type:Endothelial cell", "GSM2069437", "GSM2069437: EC con2; Danio rerio; RNA Seq", "GSM2069437", null, "1", "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", "GEO Accession:GSM2069437", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP070686", null, null, "EC-con2-SC022_2.fq.gz EC-con2-SC022_1.fq.gz", "fastq fastq", 5812259006.0, 29094912.0, "GSM2069437 r1", "0:99.88 1:99.88", "A:1668770504;C:1266987641;G:1260647092;T:1615770218;N:83551", 99, 99, null, null, 1668770504, 1266987641, 1260647092, 1615770218, 83551, "SRX1597278", "SRS1307296", "SRA356990", "GEO", "SouthWest university Of China", 2, 0.8919, 0.89162, 0.25452, 0.25485, 0.83347, 0.83392, 0.559, 0.55795, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2016-02-23", "Larval", "Larval", "Brain", "Nervous System"], [40487, "SRR3183441", "SRX1597277", "SRS1307297", "SRP070686", "PRJNA312899", "Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction", "GSE78194", "Transcriptome Analysis", "transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control   upon macrophage arrival   and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.", null, "pubmed:27156384", null, "EC ab1", "GSM2069436", null, "source name:EC ab|strain:ABGO|fluorescence:Dendra2red|lesion stg:macrophage arrival|tissue:brain|cell type:Endothelial cell", "EC ab1", "Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software  and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and |log2 ratio|\u22651 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology  http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes  http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type", "EC ab", null, "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", null, "strain:ABGO|fluorescence:Dendra2red|lesion stg:macrophage arrival|tissue:brain|cell type:Endothelial cell", "GSM2069436", "GSM2069436: EC ab1; Danio rerio; RNA Seq", "GSM2069436", null, "1", "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", "GEO Accession:GSM2069436", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP070686", null, null, "Ec-ab3-SC030_2.fq.gz Ec-ab3-SC030_1.fq.gz", "fastq fastq", 4865614309.0, 24358874.0, "GSM2069436 r1", "0:99.87 1:99.87", "A:1413472486;C:1059060950;G:1037673850;T:1355336145;N:70878", 99, 99, null, null, 1413472486, 1059060950, 1037673850, 1355336145, 70878, "SRX1597277", "SRS1307297", "SRA356990", "GEO", "SouthWest university Of China", 2, 0.87852, 0.8772, 0.28182, 0.28242, 0.89057, 0.89096, 0.73919, 0.73928, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2016-02-23", "Larval", "Larval", "Brain", "Nervous System"], [40488, "SRR3183440", "SRX1597276", "SRS1307298", "SRP070686", "PRJNA312899", "Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction", "GSE78194", "Transcriptome Analysis", "transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control   upon macrophage arrival   and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.", null, "pubmed:27156384", null, "Ec ab2", "GSM2069435", null, "source name:EC ab|strain:ABGO|fluorescence:Dendra2red|lesion stg:macrophage arrival|tissue:brain|cell type:Endothelial cell", "Ec ab2", "Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software  and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and |log2 ratio|\u22651 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology  http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes  http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type", "EC ab", null, "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", null, "strain:ABGO|fluorescence:Dendra2red|lesion stg:macrophage arrival|tissue:brain|cell type:Endothelial cell", "GSM2069435", "GSM2069435: Ec ab2; Danio rerio; RNA Seq", "GSM2069435", null, "1", "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", "GEO Accession:GSM2069435", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP070686", null, null, "Ec-ab2-SC026_2.fq.gz Ec-ab2-SC026_1.fq.gz", "fastq fastq", 6707716689.0, 33577941.0, "GSM2069435 r1", "0:99.88 1:99.88", "A:1928489398;C:1460549435;G:1448129164;T:1870450597;N:98095", 99, 99, null, null, 1928489398, 1460549435, 1448129164, 1870450597, 98095, "SRX1597276", "SRS1307298", "SRA356990", "GEO", "SouthWest university Of China", 2, 0.92184, 0.9211, 0.21351, 0.21381, 0.78242, 0.78246, 0.54924, 0.54828, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2016-02-23", "Larval", "Larval", "Brain", "Nervous System"], [40489, "SRR3183439", "SRX1597275", "SRS1307299", "SRP070686", "PRJNA312899", "Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction", "GSE78194", "Transcriptome Analysis", "transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control   upon macrophage arrival   and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.", null, "pubmed:27156384", null, "mac repair1", "GSM2069434", null, "source name:mac repair|strain:ABGO|fluorescence:Kaedared|lesion stg:macrophage traction|tissue:brain|cell type:Macrophage", "mac repair1", "Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software  and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and |log2 ratio|\u22651 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology  http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes  http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type", "mac repair", null, "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", null, "strain:ABGO|fluorescence:Kaedared|lesion stg:macrophage traction|tissue:brain|cell type:Macrophage", "GSM2069434", "GSM2069434: mac repair1; Danio rerio; RNA Seq", "GSM2069434", null, "1", "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", "GEO Accession:GSM2069434", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP070686", null, null, "mac-repair-3-11_1.fq.gz mac-repair-3-11_2.fq.gz", "fastq fastq", 4119165097.0, 20619633.0, "GSM2069434 r1", "0:99.88 1:99.88", "A:1220355632;C:853066472;G:852272936;T:1193322733;N:147324", 99, 99, null, null, 1220355632, 853066472, 852272936, 1193322733, 147324, "SRX1597275", "SRS1307299", "SRA356990", "GEO", "SouthWest university Of China", 2, 0.91892, 0.91808, 0.30064, 0.30083, 0.8379, 0.83812, 0.56301, 0.5643, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2016-02-23", "Larval", "Larval", "Brain", "Nervous System"], [40490, "SRR3183438", "SRX1597274", "SRS1307300", "SRP070686", "PRJNA312899", "Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction", "GSE78194", "Transcriptome Analysis", "transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control   upon macrophage arrival   and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.", null, "pubmed:27156384", null, "mac con1", "GSM2069433", null, "source name:mac con|strain:ABGO|fluorescence:Kaedared|lesion stg:uninjured control|tissue:brain|cell type:Macrophage", "mac con1", "Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software  and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and |log2 ratio|\u22651 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology  http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes  http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type", "mac con", null, "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", null, "strain:ABGO|fluorescence:Kaedared|lesion stg:uninjured control|tissue:brain|cell type:Macrophage", "GSM2069433", "GSM2069433: mac con1; Danio rerio; RNA Seq", "GSM2069433", null, "1", "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", "GEO Accession:GSM2069433", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP070686", null, null, "mac-con-2-26_2.fq.gz mac-con-2-26_1.fq.gz", "fastq fastq", 5593489486.0, 27999140.0, "GSM2069433 r1", "0:99.89 1:99.89", "A:1625139429;C:1195509047;G:1187687983;T:1585113551;N:39476", 99, 99, null, null, 1625139429, 1195509047, 1187687983, 1585113551, 39476, "SRX1597274", "SRS1307300", "SRA356990", "GEO", "SouthWest university Of China", 2, 0.91078, 0.91073, 0.29885, 0.30068, 0.83167, 0.83244, 0.62474, 0.6305, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2016-02-23", "Larval", "Larval", "Brain", "Nervous System"], [40491, "SRR3183437", "SRX1597273", "SRS1307301", "SRP070686", "PRJNA312899", "Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction", "GSE78194", "Transcriptome Analysis", "transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control   upon macrophage arrival   and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.", null, "pubmed:27156384", null, "mac ab1", "GSM2069432", null, "source name:mac ab|strain:ABGO|fluorescence:Kaedared|lesion stg:macrophage arrival|tissue:brain|cell type:Macrophage", "mac ab1", "Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software  and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and |log2 ratio|\u22651 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology  http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes  http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type", "mac ab", null, "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", null, "strain:ABGO|fluorescence:Kaedared|lesion stg:macrophage arrival|tissue:brain|cell type:Macrophage", "GSM2069432", "GSM2069432: mac ab1; Danio rerio; RNA Seq", "GSM2069432", null, "1", "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", "GEO Accession:GSM2069432", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP070686", null, null, "mac-ab-3-4_1.fq.gz mac-ab-3-4_2.fq.gz", "fastq fastq", 5218899449.0, 26123043.0, "GSM2069432 r1", "0:99.89 1:99.89", "A:1547095822;C:1077774232;G:1071111992;T:1522880692;N:36711", 99, 99, null, null, 1547095822, 1077774232, 1071111992, 1522880692, 36711, "SRX1597273", "SRS1307301", "SRA356990", "GEO", "SouthWest university Of China", 2, 0.80093, 0.80114, 0.34662, 0.34753, 0.84431, 0.84528, 0.45488, 0.58269, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2016-02-23", "Larval", "Larval", "Brain", "Nervous System"], [40492, "SRR3183436", "SRX1597272", "SRS1307302", "SRP070686", "PRJNA312899", "Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction", "GSE78194", "Transcriptome Analysis", "transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control   upon macrophage arrival   and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.", null, "pubmed:27156384", null, "EC repair1", "GSM2069431", null, "source name:EC repair|strain:ABGO|fluorescence:Dendra2red|lesion stg:macrophage traction|tissue:brain|cell type:Endothelial cell", "EC repair1", "Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software  and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and |log2 ratio|\u22651 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology  http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes  http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type", "EC repair", null, "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", null, "strain:ABGO|fluorescence:Dendra2red|lesion stg:macrophage traction|tissue:brain|cell type:Endothelial cell", "GSM2069431", "GSM2069431: EC repair1; Danio rerio; RNA Seq", "GSM2069431", null, "1", "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", "GEO Accession:GSM2069431", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP070686", null, null, "EC-repair-3-12_1.fq.gz EC-repair-3-12_2.fq.gz", "fastq fastq", 4074593965.0, 20396835.0, "GSM2069431 r1", "0:99.88 1:99.88", "A:1183916478;C:879516439;G:873592591;T:1137385419;N:183038", 99, 99, null, null, 1183916478, 879516439, 873592591, 1137385419, 183038, "SRX1597272", "SRS1307302", "SRA356990", "GEO", "SouthWest university Of China", 2, 0.91437, 0.91374, 0.17815, 0.179, 0.8504, 0.85141, 0.56489, 0.56038, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2016-02-23", "Larval", "Larval", "Brain", "Nervous System"], [40493, "SRR3183435", "SRX1597271", "SRS1307303", "SRP070686", "PRJNA312899", "Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction", "GSE78194", "Transcriptome Analysis", "transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control   upon macrophage arrival   and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.", null, "pubmed:27156384", null, "EC con1", "GSM2069430", null, "source name:EC con|strain:ABGO|fluorescence:Dendra2red|lesion stg:uninjured control|tissue:brain|cell type:Endothelial cell", "EC con1", "Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software  and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and |log2 ratio|\u22651 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology  http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes  http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type", "EC con", null, "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", null, "strain:ABGO|fluorescence:Dendra2red|lesion stg:uninjured control|tissue:brain|cell type:Endothelial cell", "GSM2069430", "GSM2069430: EC con1; Danio rerio; RNA Seq", "GSM2069430", null, "1", "Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control  macrophage arrival  and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion  zebrafish heads were dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500  Illumina", "GEO Accession:GSM2069430", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP070686", null, null, "EC-con-2-27_2.fq.gz", "fastq", 5255670920.0, 26309124.0, "GSM2069430 r1", "0:99.88 1:99.88", "A:1577945764;C:1073541139;G:1067712819;T:1536399615;N:71583", 99, 99, null, null, 1577945764, 1073541139, 1067712819, 1536399615, 71583, "SRX1597271", "SRS1307303", "SRA356990", "GEO", "SouthWest university Of China", 2, 0.87619, 0.87775, 0.42791, 0.42947, 0.88509, 0.88645, 0.63901, 0.63893, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2016-02-23", "Larval", "Larval", "Brain", "Nervous System"], [45062, "SRR6469875", "SRX3559780", "SRS2832982", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9784", "GSM2934373", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9784", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934373", "GSM2934373: pMH9784; Danio rerio; RNA Seq", "GSM2934373", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934373", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9784_S384_R1.fastq.gz pMH9784_S384_R2.fastq.gz", "fastq fastq", 145126332.0, 1909557.0, "GSM2934373 r1", "0:38 1:38", "A:40155475;C:32198422;G:32506219;T:40160475;N:105741", 38, 38, null, null, 40155475, 32198422, 32506219, 40160475, 105741, "SRX3559780", "SRS2832982", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.87335, 0.87266, 0.27462, 0.27905, 0.96264, 0.96449, 0.46807, 0.47208, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45063, "SRR6469874", "SRX3559779", "SRS2832983", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9783", "GSM2934372", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9783", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934372", "GSM2934372: pMH9783; Danio rerio; RNA Seq", "GSM2934372", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934372", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9783_S383_R1.fastq.gz pMH9783_S383_R2.fastq.gz", "fastq fastq", 71252128.0, 937528.0, "GSM2934372 r1", "0:38 1:38", "A:20201583;C:15281665;G:15493462;T:20226207;N:49211", 38, 38, null, null, 20201583, 15281665, 15493462, 20226207, 49211, "SRX3559779", "SRS2832983", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.85892, 0.85688, 0.36311, 0.3687, 0.95818, 0.96006, 0.45386, 0.46247, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45064, "SRR6469873", "SRX3559778", "SRS2832980", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9782", "GSM2934371", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9782", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934371", "GSM2934371: pMH9782; Danio rerio; RNA Seq", "GSM2934371", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934371", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9782_S382_R1.fastq.gz pMH9782_S382_R2.fastq.gz", "fastq fastq", 152087324.0, 2001149.0, "GSM2934371 r1", "0:38 1:38", "A:42084665;C:33681708;G:33966736;T:42249591;N:104624", 38, 38, null, null, 42084665, 33681708, 33966736, 42249591, 104624, "SRX3559778", "SRS2832980", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.87018, 0.87062, 0.27987, 0.2818, 0.95209, 0.95353, 0.51215, 0.51683, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45065, "SRR6469872", "SRX3559777", "SRS2832979", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9781", "GSM2934370", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9781", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934370", "GSM2934370: pMH9781; Danio rerio; RNA Seq", "GSM2934370", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934370", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9781_S381_R1.fastq.gz pMH9781_S381_R2.fastq.gz", "fastq fastq", 36924828.0, 485853.0, "GSM2934370 r1", "0:38 1:38", "A:10459818;C:7829499;G:7971829;T:10638782;N:24900", 38, 38, null, null, 10459818, 7829499, 7971829, 10638782, 24900, "SRX3559777", "SRS2832979", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.85066, 0.85425, 0.32934, 0.3351, 0.94586, 0.94856, 0.51047, 0.51568, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45066, "SRR6469871", "SRX3559776", "SRS2832978", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9780", "GSM2934369", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9780", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934369", "GSM2934369: pMH9780; Danio rerio; RNA Seq", "GSM2934369", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934369", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9780_S380_R1.fastq.gz pMH9780_S380_R2.fastq.gz", "fastq fastq", 119867124.0, 1577199.0, "GSM2934369 r1", "0:38 1:38", "A:33227501;C:26505020;G:26758353;T:33293693;N:82557", 38, 38, null, null, 33227501, 26505020, 26758353, 33293693, 82557, "SRX3559776", "SRS2832978", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.89197, 0.89082, 0.24603, 0.24896, 0.9695, 0.97011, 0.44946, 0.45022, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45067, "SRR6469870", "SRX3559775", "SRS2832977", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9779", "GSM2934368", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9779", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934368", "GSM2934368: pMH9779; Danio rerio; RNA Seq", "GSM2934368", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934368", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9779_S379_R1.fastq.gz pMH9779_S379_R2.fastq.gz", "fastq fastq", 46161868.0, 607393.0, "GSM2934368 r1", "0:38 1:38", "A:13078027;C:9898117;G:10038211;T:13116286;N:31227", 38, 38, null, null, 13078027, 9898117, 10038211, 13116286, 31227, "SRX3559775", "SRS2832977", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.85996, 0.85997, 0.29607, 0.29933, 0.94819, 0.94988, 0.47528, 0.47648, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45068, "SRR6469869", "SRX3559774", "SRS2832975", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9778", "GSM2934367", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9778", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934367", "GSM2934367: pMH9778; Danio rerio; RNA Seq", "GSM2934367", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934367", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9778_S378_R1.fastq.gz pMH9778_S378_R2.fastq.gz", "fastq fastq", 122849060.0, 1616435.0, "GSM2934367 r1", "0:38 1:38", "A:33299008;C:27904479;G:28236970;T:33321198;N:87405", 38, 38, null, null, 33299008, 27904479, 28236970, 33321198, 87405, "SRX3559774", "SRS2832975", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.87661, 0.87551, 0.23309, 0.23606, 0.97319, 0.97398, 0.49341, 0.50469, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45069, "SRR6469868", "SRX3559773", "SRS2832998", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9777", "GSM2934366", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9777", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934366", "GSM2934366: pMH9777; Danio rerio; RNA Seq", "GSM2934366", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934366", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9777_S377_R1.fastq.gz pMH9777_S377_R2.fastq.gz", "fastq fastq", 4000032.0, 52632.0, "GSM2934366 r1", "0:38 1:38", "A:1031489;C:888762;G:946282;T:1130745;N:2754", 38, 38, null, null, 1031489, 888762, 946282, 1130745, 2754, "SRX3559773", "SRS2832998", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.04841, 0.03065, 0.04352, 0.02645, 0.99839, 0.99904, 0.63228, 0.58278, 38, 38, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45070, "SRR6469867", "SRX3559772", "SRS2833004", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9776", "GSM2934365", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9776", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934365", "GSM2934365: pMH9776; Danio rerio; RNA Seq", "GSM2934365", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934365", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9776_S376_R1.fastq.gz pMH9776_S376_R2.fastq.gz", "fastq fastq", 44033564.0, 579389.0, "GSM2934365 r1", "0:38 1:38", "A:12066340;C:9847538;G:9938961;T:12149091;N:31634", 38, 38, null, null, 12066340, 9847538, 9938961, 12149091, 31634, "SRX3559772", "SRS2833004", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.86208, 0.86417, 0.25113, 0.25215, 0.96169, 0.96266, 0.42688, 0.44982, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45071, "SRR6469866", "SRX3559771", "SRS2832974", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9775", "GSM2934364", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9775", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934364", "GSM2934364: pMH9775; Danio rerio; RNA Seq", "GSM2934364", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9774", "GSM2934363", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9774", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934363", "GSM2934363: pMH9774; Danio rerio; RNA Seq", "GSM2934363", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934363", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9774_S374_R1.fastq.gz pMH9774_S374_R2.fastq.gz", "fastq fastq", 154811468.0, 2036993.0, "GSM2934363 r1", "0:38 1:38", "A:41561871;C:35642962;G:35960434;T:41539597;N:106604", 38, 38, null, null, 41561871, 35642962, 35960434, 41539597, 106604, "SRX3559770", "SRS2833005", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.91203, 0.91075, 0.16707, 0.17069, 0.95625, 0.95771, 0.4676, 0.48663, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45073, "SRR6469864", "SRX3559769", "SRS2832976", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9773", "GSM2934362", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9773", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934362", "GSM2934362: pMH9773; Danio rerio; RNA Seq", "GSM2934362", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934362", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9773_S373_R1.fastq.gz pMH9773_S373_R2.fastq.gz", "fastq fastq", 86503428.0, 1138203.0, "GSM2934362 r1", "0:38 1:38", "A:23603486;C:19465061;G:19755089;T:23617043;N:62749", 38, 38, null, null, 23603486, 19465061, 19755089, 23617043, 62749, "SRX3559769", "SRS2832976", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.82688, 0.82489, 0.28334, 0.28923, 0.94856, 0.95043, 0.47916, 0.47164, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45074, "SRR6469863", "SRX3559768", "SRS2832989", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9772", "GSM2934361", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9772", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934361", "GSM2934361: pMH9772; Danio rerio; RNA Seq", "GSM2934361", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9771", "GSM2934360", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9771", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934360", "GSM2934360: pMH9771; Danio rerio; RNA Seq", "GSM2934360", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934360", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9771_S371_R1.fastq.gz pMH9771_S371_R2.fastq.gz", "fastq fastq", 77825368.0, 1024018.0, "GSM2934360 r1", "0:38 1:38", "A:21420768;C:17362216;G:17622220;T:21366208;N:53956", 38, 38, null, null, 21420768, 17362216, 17622220, 21366208, 53956, "SRX3559767", "SRS2832973", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.81073, 0.81018, 0.31645, 0.32191, 0.95584, 0.95735, 0.45909, 0.46416, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45076, "SRR6469861", "SRX3559766", "SRS2833006", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9770", "GSM2934359", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9770", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934359", "GSM2934359: pMH9770; Danio rerio; RNA Seq", "GSM2934359", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9769", "GSM2934358", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9769", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934358", "GSM2934358: pMH9769; Danio rerio; RNA Seq", "GSM2934358", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934358", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9769_S369_R1.fastq.gz pMH9769_S369_R2.fastq.gz", "fastq fastq", 96363212.0, 1267937.0, "GSM2934358 r1", "0:38 1:38", "A:26140520;C:21944356;G:22177415;T:26034240;N:66681", 38, 38, null, null, 26140520, 21944356, 22177415, 26034240, 66681, "SRX3559765", "SRS2832990", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.87404, 0.87374, 0.24433, 0.24521, 0.90567, 0.90774, 0.50778, 0.5063, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45078, "SRR6469859", "SRX3559764", "SRS2832972", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9768", "GSM2934357", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9768", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934357", "GSM2934357: pMH9768; Danio rerio; RNA Seq", "GSM2934357", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9767", "GSM2934356", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9767", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934356", "GSM2934356: pMH9767; Danio rerio; RNA Seq", "GSM2934356", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9766", "GSM2934355", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9766", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934355", "GSM2934355: pMH9766; Danio rerio; RNA Seq", "GSM2934355", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934355", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9766_S366_R1.fastq.gz pMH9766_S366_R2.fastq.gz", "fastq fastq", 122313260.0, 1609385.0, "GSM2934355 r1", "0:38 1:38", "A:32924395;C:28095371;G:28378377;T:32827985;N:87132", 38, 38, null, null, 32924395, 28095371, 28378377, 32827985, 87132, "SRX3559762", "SRS2832970", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.89473, 0.89244, 0.27457, 0.27829, 0.96252, 0.96412, 0.50325, 0.49308, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45081, "SRR6469856", "SRX3559761", "SRS2832965", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9765", "GSM2934354", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9765", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9764", "GSM2934353", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9764", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9763", "GSM2934352", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9763", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934352", "GSM2934352: pMH9763; Danio rerio; RNA Seq", "GSM2934352", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934352", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9763_S363_R1.fastq.gz pMH9763_S363_R2.fastq.gz", "fastq fastq", 87598284.0, 1152609.0, "GSM2934352 r1", "0:38 1:38", "A:24363101;C:19246802;G:19619641;T:24308269;N:60471", 38, 38, null, null, 24363101, 19246802, 19619641, 24308269, 60471, "SRX3559759", "SRS2832968", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.80411, 0.80234, 0.33918, 0.34196, 0.95093, 0.95254, 0.47454, 0.46732, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45084, "SRR6469853", "SRX3559758", "SRS2832969", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9762", "GSM2934351", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9762", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934351", "GSM2934351: pMH9762; Danio rerio; RNA Seq", "GSM2934351", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9761", "GSM2934350", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9761", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934350", "GSM2934350: pMH9761; Danio rerio; RNA Seq", "GSM2934350", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9760", "GSM2934349", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9760", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934349", "GSM2934349: pMH9760; Danio rerio; RNA Seq", "GSM2934349", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934349", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9760_S360_R1.fastq.gz pMH9760_S360_R2.fastq.gz", "fastq fastq", 69160.0, 910.0, "GSM2934349 r1", "0:38 1:38", "A:24687;C:14606;G:11964;T:17838;N:65", 38, 38, null, null, 24687, 14606, 11964, 17838, 65, "SRX3559756", "SRS2833009", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.8029, 0.81082, 0.20869, 0.21621, 0.99655, 0.99955, 0.55121, 0.54545, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45087, "SRR6469850", "SRX3559755", "SRS2832967", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9759", "GSM2934348", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9759", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934348", "GSM2934348: pMH9759; Danio rerio; RNA Seq", "GSM2934348", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9758", "GSM2934347", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9758", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934347", "GSM2934347: pMH9758; Danio rerio; RNA Seq", "GSM2934347", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9757", "GSM2934346", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9757", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9756", "GSM2934345", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9756", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9755", "GSM2934344", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9755", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934344", "GSM2934344: pMH9755; Danio rerio; RNA Seq", "GSM2934344", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934344", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9755_S355_R1.fastq.gz pMH9755_S355_R2.fastq.gz", "fastq fastq", 131362580.0, 1728455.0, "GSM2934344 r1", "0:38 1:38", "A:34578854;C:30893838;G:31258520;T:34536804;N:94564", 38, 38, null, null, 34578854, 30893838, 31258520, 34536804, 94564, "SRX3559751", "SRS2832957", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.88124, 0.88158, 0.25279, 0.25873, 0.95645, 0.95818, 0.46594, 0.4679, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45092, "SRR6469845", "SRX3559750", "SRS2832956", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9754", "GSM2934343", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9754", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9753", "GSM2934342", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9753", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934342", "GSM2934342: pMH9753; Danio rerio; RNA Seq", "GSM2934342", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9752", "GSM2934341", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9752", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934341", "GSM2934341: pMH9752; Danio rerio; RNA Seq", "GSM2934341", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9751", "GSM2934340", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9751", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9750", "GSM2934339", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9750", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9749", "GSM2934338", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9749", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9748", "GSM2934337", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9748", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9747", "GSM2934336", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9747", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934336", "GSM2934336: pMH9747; Danio rerio; RNA Seq", "GSM2934336", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934336", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9747_S347_R1.fastq.gz pMH9747_S347_R2.fastq.gz", "fastq fastq", 150201840.0, 1976340.0, "GSM2934336 r1", "0:38 1:38", "A:40400461;C:34530136;G:34847440;T:40320690;N:103113", 38, 38, null, null, 40400461, 34530136, 34847440, 40320690, 103113, "SRX3559743", "SRS2832949", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.8939, 0.89143, 0.23725, 0.24102, 0.95199, 0.95406, 0.46307, 0.47718, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45100, "SRR6469837", "SRX3559742", "SRS2832950", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9746", "GSM2934335", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9746", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9745", "GSM2934334", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9745", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934334", "GSM2934334: pMH9745; Danio rerio; RNA Seq", "GSM2934334", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9744", "GSM2934333", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9744", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934333", "GSM2934333: pMH9744; Danio rerio; RNA Seq", "GSM2934333", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934333", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9744_S344_R1.fastq.gz pMH9744_S344_R2.fastq.gz", "fastq fastq", 89972372.0, 1183847.0, "GSM2934333 r1", "0:38 1:38", "A:24135638;C:20769508;G:20962914;T:24040208;N:64104", 38, 38, null, null, 24135638, 20769508, 20962914, 24040208, 64104, "SRX3559740", "SRS2832947", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.86439, 0.86363, 0.27302, 0.27765, 0.95574, 0.95828, 0.42181, 0.44263, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45103, "SRR6469834", "SRX3559739", "SRS2832945", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9743", "GSM2934332", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9743", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9742", "GSM2934331", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9742", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9741", "GSM2934330", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9741", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9740", "GSM2934329", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9740", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9739", "GSM2934328", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9739", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934328", "GSM2934328: pMH9739; Danio rerio; RNA Seq", "GSM2934328", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934328", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9739_S339_R1.fastq.gz pMH9739_S339_R2.fastq.gz", "fastq fastq", 52679324.0, 693149.0, "GSM2934328 r1", "0:38 1:38", "A:13455357;C:12823609;G:12911202;T:13456614;N:32542", 38, 38, null, null, 13455357, 12823609, 12911202, 13456614, 32542, "SRX3559735", "SRS2832943", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.65867, 0.65967, 0.19546, 0.19208, 0.93671, 0.94178, 0.53562, 0.52446, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45108, "SRR6469829", "SRX3559734", "SRS2832948", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9738", "GSM2934327", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9738", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934327", "GSM2934327: pMH9738; Danio rerio; RNA Seq", "GSM2934327", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9737", "GSM2934326", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9737", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934326", "GSM2934326: pMH9737; Danio rerio; RNA Seq", "GSM2934326", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9736", "GSM2934325", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9736", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934325", "GSM2934325: pMH9736; Danio rerio; RNA Seq", "GSM2934325", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934325", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9736_S336_R1.fastq.gz pMH9736_S336_R2.fastq.gz", "fastq fastq", 112947324.0, 1486149.0, "GSM2934325 r1", "0:38 1:38", "A:31383355;C:24926902;G:25232589;T:31326396;N:78082", 38, 38, null, null, 31383355, 24926902, 25232589, 31326396, 78082, "SRX3559732", "SRS2832940", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.87161, 0.86977, 0.30543, 0.30805, 0.96025, 0.96197, 0.4653, 0.458, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45111, "SRR6469826", "SRX3559731", "SRS2832936", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9735", "GSM2934324", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9735", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934324", "GSM2934324: pMH9735; Danio rerio; RNA Seq", "GSM2934324", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934324", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9735_S335_R1.fastq.gz pMH9735_S335_R2.fastq.gz", "fastq fastq", 71141092.0, 936067.0, "GSM2934324 r1", "0:38 1:38", "A:19757889;C:15659226;G:15880734;T:19793388;N:49855", 38, 38, null, null, 19757889, 15659226, 15880734, 19793388, 49855, "SRX3559731", "SRS2832936", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.86357, 0.86251, 0.26268, 0.26695, 0.93876, 0.94095, 0.48189, 0.49983, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45112, "SRR6469825", "SRX3559730", "SRS2832939", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9734", "GSM2934323", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9734", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934323", "GSM2934323: pMH9734; Danio rerio; RNA Seq", "GSM2934323", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934323", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9734_S334_R1.fastq.gz pMH9734_S334_R2.fastq.gz", "fastq fastq", 141032136.0, 1855686.0, "GSM2934323 r1", "0:38 1:38", "A:38879528;C:31421074;G:31701658;T:38931853;N:98023", 38, 38, null, null, 38879528, 31421074, 31701658, 38931853, 98023, "SRX3559730", "SRS2832939", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.88384, 0.88264, 0.25041, 0.25216, 0.94911, 0.95162, 0.4681, 0.4777, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45113, "SRR6469824", "SRX3559729", "SRS2832954", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9733", "GSM2934322", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9733", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9732", "GSM2934321", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9732", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9731", "GSM2934320", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9731", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934320", "GSM2934320: pMH9731; Danio rerio; RNA Seq", "GSM2934320", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934320", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9731_S331_R1.fastq.gz pMH9731_S331_R2.fastq.gz", "fastq fastq", 60045928.0, 790078.0, "GSM2934320 r1", "0:38 1:38", "A:16950488;C:12918057;G:13106622;T:17029402;N:41359", 38, 38, null, null, 16950488, 12918057, 13106622, 17029402, 41359, "SRX3559727", "SRS2832934", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.86384, 0.86201, 0.32944, 0.33464, 0.95519, 0.95706, 0.44738, 0.46308, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45116, "SRR6469821", "SRX3559726", "SRS2832933", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9730", "GSM2934319", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9730", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934319", "GSM2934319: pMH9730; Danio rerio; RNA Seq", "GSM2934319", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934319", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9730_S330_R1.fastq.gz pMH9730_S330_R2.fastq.gz", "fastq fastq", 57116660.0, 751535.0, "GSM2934319 r1", "0:38 1:38", "A:15821926;C:12604434;G:12765205;T:15883566;N:41529", 38, 38, null, null, 15821926, 12604434, 12765205, 15883566, 41529, "SRX3559726", "SRS2832933", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.86383, 0.86324, 0.33014, 0.33079, 0.97179, 0.97313, 0.44322, 0.44641, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45117, "SRR6469820", "SRX3559725", "SRS2832935", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9729", "GSM2934318", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9729", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934318", "GSM2934318: pMH9729; Danio rerio; RNA Seq", "GSM2934318", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934318", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9729_S329_R1.fastq.gz pMH9729_S329_R2.fastq.gz", "fastq fastq", 77538392.0, 1020242.0, "GSM2934318 r1", "0:38 1:38", "A:21386632;C:17249157;G:17451599;T:21396687;N:54317", 38, 38, null, null, 21386632, 17249157, 17451599, 21396687, 54317, "SRX3559725", "SRS2832935", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.88693, 0.88697, 0.25229, 0.25798, 0.92967, 0.93178, 0.5065, 0.50201, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45118, "SRR6469819", "SRX3559724", "SRS2832930", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9728", "GSM2934317", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9728", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934317", "GSM2934317: pMH9728; Danio rerio; RNA Seq", "GSM2934317", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934317", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9728_S328_R1.fastq.gz pMH9728_S328_R2.fastq.gz", "fastq fastq", 106709320.0, 1404070.0, "GSM2934317 r1", "0:38 1:38", "A:29536478;C:23638374;G:23867439;T:29593490;N:73539", 38, 38, null, null, 29536478, 23638374, 23867439, 29593490, 73539, "SRX3559724", "SRS2832930", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.86686, 0.86665, 0.31028, 0.31128, 0.96412, 0.96526, 0.47478, 0.48512, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45119, "SRR6469818", "SRX3559723", "SRS2832931", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9727", "GSM2934316", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9727", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934316", "GSM2934316: pMH9727; Danio rerio; RNA Seq", "GSM2934316", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934316", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9727_S327_R1.fastq.gz pMH9727_S327_R2.fastq.gz", "fastq fastq", 86095688.0, 1132838.0, "GSM2934316 r1", "0:38 1:38", "A:23847680;C:19059455;G:19282417;T:23845385;N:60751", 38, 38, null, null, 23847680, 19059455, 19282417, 23845385, 60751, "SRX3559723", "SRS2832931", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.83953, 0.83898, 0.30341, 0.30275, 0.95101, 0.95258, 0.49718, 0.51199, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45120, "SRR6469817", "SRX3559722", "SRS2832937", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9726", "GSM2934315", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9726", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934315", "GSM2934315: pMH9726; Danio rerio; RNA Seq", "GSM2934315", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934315", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9726_S326_R1.fastq.gz pMH9726_S326_R2.fastq.gz", "fastq fastq", 139600828.0, 1836853.0, "GSM2934315 r1", "0:38 1:38", "A:38597826;C:30866718;G:31368939;T:38668190;N:99155", 38, 38, null, null, 38597826, 30866718, 31368939, 38668190, 99155, "SRX3559722", "SRS2832937", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.86621, 0.8641, 0.33142, 0.33249, 0.96938, 0.96958, 0.50699, 0.50069, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45121, "SRR6469816", "SRX3559721", "SRS2832932", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9725", "GSM2934314", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9725", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934314", "GSM2934314: pMH9725; Danio rerio; RNA Seq", "GSM2934314", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934314", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9725_S325_R1.fastq.gz pMH9725_S325_R2.fastq.gz", "fastq fastq", 121083960.0, 1593210.0, "GSM2934314 r1", "0:38 1:38", "A:32899764;C:27378986;G:27823239;T:32898732;N:83239", 38, 38, null, null, 32899764, 27378986, 27823239, 32898732, 83239, "SRX3559721", "SRS2832932", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.80328, 0.79995, 0.30294, 0.30555, 0.95899, 0.96079, 0.46157, 0.47033, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45122, "SRR6469815", "SRX3559720", "SRS2832928", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9724", "GSM2934313", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9724", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934313", "GSM2934313: pMH9724; Danio rerio; RNA Seq", "GSM2934313", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", "GEO Accession:GSM2934313", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP129440", null, null, "pMH9724_S324_R1.fastq.gz pMH9724_S324_R2.fastq.gz", "fastq fastq", 92381116.0, 1215541.0, "GSM2934313 r1", "0:38 1:38", "A:24013740;C:22035732;G:22292307;T:23975988;N:63349", 38, 38, null, null, 24013740, 22035732, 22292307, 23975988, 63349, "SRX3559720", "SRS2832928", "SRA646358", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 2, 0.56536, 0.56858, 0.20377, 0.20826, 0.95716, 0.95875, 0.47084, 0.47638, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-01-12", "Larval", "Larval", "Brain", "Nervous System"], [45123, "SRR6469814", "SRX3559719", "SRS2832927", "SRP129440", "PRJNA429937", "Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line", "GSE109159", "Transcriptome Analysis", "The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9723", "GSM2934312", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9723", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  Nature Methods  2014", null, "genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula", "GSM2934312", "GSM2934312: pMH9723; Danio rerio; RNA Seq", "GSM2934312", null, "1", "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9722", "GSM2934311", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9722", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9721", "GSM2934310", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9721", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9720", "GSM2934309", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9720", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected  dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2.", "parent bioproject:PRJNA414719", "pubmed:29576475", null, "pMH9719", "GSM2934308", null, "source name:Danio Rerio  10dpf GFP|tissue:brain|cell type:10dpf habenula", "pMH9719", "Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters", "Danio Rerio  10dpf", null, "Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al.  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