{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Multi-stage\" and tissue_curation_coarse = \"Sensory System\"", "rows": [[33202, "SRR29848463", "SRX25346228", "SRS22013442", "SRP520276", "PRJNA1136505", "Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish", "GSE272355", "Transcriptome Analysis", "Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylomic regulation. Finally we observed that IPP affects gene expression within the developing eye establishing synaptic transmission vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf eyes and brains were dissected out RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina San Diego CA 2x150 bp 40m reads/sample.", null, "pubmed:39742644", null, "IPP 120hpf eye replicate4", "GSM8399280", null, "source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf|geo loc name:missing|collection date:missing", "IPP 120hpf eye replicate4", "Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. 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The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylomic regulation. Finally we observed that IPP affects gene expression within the developing eye establishing synaptic transmission vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf eyes and brains were dissected out RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina San Diego CA 2x150 bp 40m reads/sample.", null, "pubmed:39742644", null, "IPP 120hpf eye replicate3", "GSM8399279", null, "source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf|geo loc name:missing|collection date:missing", "IPP 120hpf eye replicate3", "Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample", "Dissected eye", "Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf", "Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. 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The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylomic regulation. Finally we observed that IPP affects gene expression within the developing eye establishing synaptic transmission vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf eyes and brains were dissected out RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina San Diego CA 2x150 bp 40m reads/sample.", null, "pubmed:39742644", null, "IPP 120hpf eye replicate2", "GSM8399278", null, "source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf|geo loc name:missing|collection date:missing", "IPP 120hpf eye replicate2", "Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample", "Dissected eye", "Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf", "Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. 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The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylomic regulation. Finally we observed that IPP affects gene expression within the developing eye establishing synaptic transmission vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf eyes and brains were dissected out RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina San Diego CA 2x150 bp 40m reads/sample.", null, "pubmed:39742644", null, "IPP 120hpf eye replicate1", "GSM8399277", null, "source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf|geo loc name:missing|collection date:missing", "IPP 120hpf eye replicate1", "Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample", "Dissected eye", "Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf", "Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. 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The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylomic regulation. Finally we observed that IPP affects gene expression within the developing eye establishing synaptic transmission vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf eyes and brains were dissected out RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina San Diego CA 2x150 bp 40m reads/sample.", null, "pubmed:39742644", null, "DMSO 120hpf eye replicate4", "GSM8399276", null, "source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf|geo loc name:missing|collection date:missing", "DMSO 120hpf eye replicate4", "Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample", "Dissected eye", "Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf", "Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. 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RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP520276", null, null, "Ctrl_eye_4_1.fq.gz Ctrl_eye_4_2.fq.gz", "fastq fastq", 7198057200.0, 23993524.0, "GSM8399276 r1", "0:150 1:150", "A:1929066670;C:1680279530;G:1672121671;T:1910263876;N:6325453", 150, 150, null, null, 1929066670, 1680279530, 1672121671, 1910263876, 6325453, "SRX25346224", "SRS22013438", "SRA1925887", "Dasgupta lab, Biological Sciences, Clemson University", "Dasgupta lab, Biological Sciences, Clemson University", 2, 0.91947, 0.90384, 0.11309, 0.11094, 0.69576, 0.69779, 0.45803, 0.45394, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-07-16", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [33207, "SRR29848468", "SRX25346223", "SRS22013437", "SRP520276", "PRJNA1136505", "Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish", "GSE272355", "Transcriptome Analysis", "Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylomic regulation. Finally we observed that IPP affects gene expression within the developing eye establishing synaptic transmission vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf eyes and brains were dissected out RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina San Diego CA 2x150 bp 40m reads/sample.", null, "pubmed:39742644", null, "DMSO 120hpf eye replicate3", "GSM8399275", null, "source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf|geo loc name:missing|collection date:missing", "DMSO 120hpf eye replicate3", "Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample", "Dissected eye", "Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf", "Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification", "Embryos were spawned and maintained in system water", "tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf", "GSM8399275", "GSM8399275: DMSO 120hpf eye replicate3; Danio rerio; RNA Seq", "GSM8399275 r1", "GSM8399275", "1", "Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP520276", null, null, "Ctrl_eye_3_1.fq.gz Ctrl_eye_3_2.fq.gz", "fastq fastq", 6349681200.0, 21165604.0, "GSM8399275 r1", "0:150 1:150", "A:1713020668;C:1474226584;G:1462505802;T:1694350186;N:5577960", 150, 150, null, null, 1713020668, 1474226584, 1462505802, 1694350186, 5577960, "SRX25346223", "SRS22013437", "SRA1925887", "Dasgupta lab, Biological Sciences, Clemson University", "Dasgupta lab, Biological Sciences, Clemson University", 2, 0.89548, 0.89606, 0.09628, 0.09664, 0.71102, 0.71161, 0.44199, 0.4354, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-07-16", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [33208, "SRR29848469", "SRX25346222", "SRS22013436", "SRP520276", "PRJNA1136505", "Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish", "GSE272355", "Transcriptome Analysis", "Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylomic regulation. Finally we observed that IPP affects gene expression within the developing eye establishing synaptic transmission vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf eyes and brains were dissected out RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina San Diego CA 2x150 bp 40m reads/sample.", null, "pubmed:39742644", null, "DMSO 120hpf eye replicate2", "GSM8399274", null, "source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf|geo loc name:missing|collection date:missing", "DMSO 120hpf eye replicate2", "Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample", "Dissected eye", "Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf", "Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification", "Embryos were spawned and maintained in system water", "tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf", "GSM8399274", "GSM8399274: DMSO 120hpf eye replicate2; Danio rerio; RNA Seq", "GSM8399274 r1", "GSM8399274", "1", "Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP520276", null, null, "Ctrl_eye_2_1.fq.gz Ctrl_eye_2_2.fq.gz", "fastq fastq", 6861299400.0, 22870998.0, "GSM8399274 r1", "0:150 1:150", "A:1839006136;C:1604484415;G:1591747628;T:1820307442;N:5753779", 150, 150, null, null, 1839006136, 1604484415, 1591747628, 1820307442, 5753779, "SRX25346222", "SRS22013436", "SRA1925887", "Dasgupta lab, Biological Sciences, Clemson University", "Dasgupta lab, Biological Sciences, Clemson University", 2, 0.84164, 0.83344, 0.09914, 0.09758, 0.72034, 0.72088, 0.44273, 0.4389, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-07-16", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [33209, "SRR29848470", "SRX25346221", "SRS22013435", "SRP520276", "PRJNA1136505", "Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish", "GSE272355", "Transcriptome Analysis", "Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylomic regulation. Finally we observed that IPP affects gene expression within the developing eye establishing synaptic transmission vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf eyes and brains were dissected out RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina San Diego CA 2x150 bp 40m reads/sample.", null, "pubmed:39742644", null, "DMSO 120hpf eye replicate1", "GSM8399273", null, "source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf|geo loc name:missing|collection date:missing", "DMSO 120hpf eye replicate1", "Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample", "Dissected eye", "Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf", "Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification", "Embryos were spawned and maintained in system water", "tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf", "GSM8399273", "GSM8399273: DMSO 120hpf eye replicate1; Danio rerio; RNA Seq", "GSM8399273 r1", "GSM8399273", "1", "Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP520276", null, null, "Ctrl_eye_1_1.fq.gz Ctrl_eye_1_2.fq.gz", "fastq fastq", 6544491000.0, 21814970.0, "GSM8399273 r1", "0:150 1:150", "A:1774622867;C:1510819173;G:1498655117;T:1754689449;N:5704394", 150, 150, null, null, 1774622867, 1510819173, 1498655117, 1754689449, 5704394, "SRX25346221", "SRS22013435", "SRA1925887", "Dasgupta lab, Biological Sciences, Clemson University", "Dasgupta lab, Biological Sciences, Clemson University", 2, 0.86147, 0.86095, 0.11217, 0.11159, 0.71319, 0.71352, 0.44434, 0.43886, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-07-16", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [33274, "SRR29884407", "SRX25380711", "SRS22046064", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Male 5", "GSM8406321", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Male 5", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406321", "GSM8406321: Brain wh5 Male 5; Danio rerio; RNA Seq", "GSM8406321 r1", "GSM8406321", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample20KOMaleBrain_R1.fastq Sample20KOMaleBrain_R2.fastq", "fastq fastq", 5509276088.0, 27917150.0, "GSM8406321 r1", "0:98.67 1:98.67", "A:1498190193;C:1242495192;G:1267229536;T:1499431726;N:1929441", 98, 98, null, null, 1498190193, 1242495192, 1267229536, 1499431726, 1929441, "SRX25380711", "SRS22046064", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94576, 0.94515, 0.14102, 0.13871, 0.69187, 0.69077, 0.52554, 0.53007, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33275, "SRR29884408", "SRX25380710", "SRS22046063", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Male 4", "GSM8406320", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Male 4", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406320", "GSM8406320: Brain wh5 Male 4; Danio rerio; RNA Seq", "GSM8406320 r1", "GSM8406320", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample19KOMaleBrain_R1.fastq Sample19KOMaleBrain_R2.fastq", "fastq fastq", 6985356408.0, 35379007.0, "GSM8406320 r1", "0:98.72 1:98.72", "A:1889039547;C:1582622229;G:1620512342;T:1890746302;N:2435988", 98, 98, null, null, 1889039547, 1582622229, 1620512342, 1890746302, 2435988, "SRX25380710", "SRS22046063", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94197, 0.94411, 0.14763, 0.14597, 0.69852, 0.69826, 0.54705, 0.54822, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33276, "SRR29884409", "SRX25380709", "SRS22046062", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Male 3", "GSM8406319", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Male 3", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406319", "GSM8406319: Brain wh5 Male 3; Danio rerio; RNA Seq", "GSM8406319 r1", "GSM8406319", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample18KOMaleBrain_R1.fastq Sample18KOMaleBrain_R2.fastq", "fastq fastq", 5864072768.0, 29837549.0, "GSM8406319 r1", "0:98.27 1:98.27", "A:1609423180;C:1310248473;G:1328624911;T:1613750029;N:2026175", 98, 98, null, null, 1609423180, 1310248473, 1328624911, 1613750029, 2026175, "SRX25380709", "SRS22046062", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94007, 0.94233, 0.14021, 0.1386, 0.69376, 0.69317, 0.51507, 0.52214, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33277, "SRR29884410", "SRX25380708", "SRS22046061", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Male 2", "GSM8406318", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Male 2", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406318", "GSM8406318: Brain wh5 Male 2; Danio rerio; RNA Seq", "GSM8406318 r1", "GSM8406318", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample17KOMaleBrain_R1.fastq Sample17KOMaleBrain_R2.fastq", "fastq fastq", 5841328432.0, 29860768.0, "GSM8406318 r1", "0:97.81 1:97.81", "A:1606036785;C:1302920703;G:1321021765;T:1609306125;N:2043054", 97, 97, null, null, 1606036785, 1302920703, 1321021765, 1609306125, 2043054, "SRX25380708", "SRS22046061", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.9429, 0.94295, 0.14247, 0.14023, 0.69808, 0.69739, 0.51804, 0.51798, 69, 69, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33278, "SRR29884411", "SRX25380707", "SRS22046060", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Male 1", "GSM8406317", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Male 1", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406317", "GSM8406317: Brain wh5 Male 1; Danio rerio; RNA Seq", "GSM8406317 r1", "GSM8406317", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample16KOMaleBrain_R1.fastq Sample16KOMaleBrain_R2.fastq", "fastq fastq", 6061816166.0, 30929476.0, "GSM8406317 r1", "0:97.99 1:97.99", "A:1666435568;C:1352308656;G:1373281492;T:1667671946;N:2118504", 97, 97, null, null, 1666435568, 1352308656, 1373281492, 1667671946, 2118504, "SRX25380707", "SRS22046060", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94198, 0.9434, 0.14745, 0.14621, 0.69201, 0.69138, 0.52388, 0.52247, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33279, "SRR29884412", "SRX25380706", "SRS22046059", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Female 5", "GSM8406316", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Female 5", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406316", "GSM8406316: Brain wh5 Female 5; Danio rerio; RNA Seq", "GSM8406316 r1", "GSM8406316", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample15KOFemaleBrain_R1.fastq Sample15KOFemaleBrain_R2.fastq", "fastq fastq", 5830172008.0, 29715950.0, "GSM8406316 r1", "0:98.10 1:98.10", "A:1585225847;C:1316585087;G:1339955604;T:1586384657;N:2020813", 98, 98, null, null, 1585225847, 1316585087, 1339955604, 1586384657, 2020813, "SRX25380706", "SRS22046059", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94307, 0.94571, 0.13598, 0.13423, 0.69341, 0.69309, 0.52103, 0.50706, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33280, "SRR29884413", "SRX25380705", "SRS22046058", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Female 4", "GSM8406315", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Female 4", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406315", "GSM8406315: Brain wh5 Female 4; Danio rerio; RNA Seq", "GSM8406315 r1", "GSM8406315", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample14KOFemaleBrain_R1.fastq Sample14KOFemaleBrain_R2.fastq", "fastq fastq", 6700791892.0, 34096304.0, "GSM8406315 r1", "0:98.26 1:98.26", "A:1817874372;C:1516000049;G:1546573687;T:1818017657;N:2326127", 98, 98, null, null, 1817874372, 1516000049, 1546573687, 1818017657, 2326127, "SRX25380705", "SRS22046058", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94342, 0.94623, 0.13719, 0.13523, 0.69313, 0.69254, 0.53293, 0.53816, 84, 84, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33281, "SRR29884414", "SRX25380704", "SRS22046057", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Female 3", "GSM8406314", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Female 3", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406314", "GSM8406314: Brain wh5 Female 3; Danio rerio; RNA Seq", "GSM8406314 r1", "GSM8406314", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample13KOFemaleBrain_R2.fastq Sample13KOFemaleBrain_R1.fastq", "fastq fastq", 6308152444.0, 32040291.0, "GSM8406314 r1", "0:98.44 1:98.44", "A:1698706705;C:1436132175;G:1472501608;T:1698611730;N:2200226", 98, 98, null, null, 1698706705, 1436132175, 1472501608, 1698611730, 2200226, "SRX25380704", "SRS22046057", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94654, 0.94476, 0.1362, 0.13304, 0.694, 0.69321, 0.54515, 0.53479, 91, 91, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33282, "SRR29884415", "SRX25380703", "SRS22046056", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Female 2", "GSM8406313", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Female 2", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406313", "GSM8406313: Brain wh5 Female 2; Danio rerio; RNA Seq", "GSM8406313 r1", "GSM8406313", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample12KOFemaleBrain_R1.fastq Sample12KOFemaleBrain_R2.fastq", "fastq fastq", 6503673262.0, 33197897.0, "GSM8406313 r1", "0:97.95 1:97.95", "A:1781196226;C:1457467194;G:1479672271;T:1783090598;N:2246973", 97, 97, null, null, 1781196226, 1457467194, 1479672271, 1783090598, 2246973, "SRX25380703", "SRS22046056", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94227, 0.94462, 0.13793, 0.13614, 0.69359, 0.69355, 0.52971, 0.52982, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33283, "SRR29884416", "SRX25380702", "SRS22046055", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Female 1", "GSM8406312", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Female 1", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406312", "GSM8406312: Brain wh5 Female 1; Danio rerio; RNA Seq", "GSM8406312 r1", "GSM8406312", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample11KOFemaleBrain_R1.fastq Sample11KOFemaleBrain_R2.fastq", "fastq fastq", 5803578222.0, 29408217.0, "GSM8406312 r1", "0:98.67 1:98.67", "A:1586553028;C:1303184285;G:1323602566;T:1588219875;N:2018468", 98, 98, null, null, 1586553028, 1303184285, 1323602566, 1588219875, 2018468, "SRX25380702", "SRS22046055", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94183, 0.94513, 0.1442, 0.14286, 0.6942, 0.6942, 0.51627, 0.51673, 93, 93, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33284, "SRR29884417", "SRX25380701", "SRS22046053", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Male 5", "GSM8406311", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Male 5", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406311", "GSM8406311: Brain WT Male 5; Danio rerio; RNA Seq", "GSM8406311 r1", "GSM8406311", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample10WTMaleBrain_R1.fastq Sample10WTMaleBrain_R2.fastq", "fastq fastq", 4558024898.0, 24051338.0, "GSM8406311 r1", "0:94.76 1:94.76", "A:1220269093;C:1048518583;G:1068311203;T:1219299559;N:1626460", 94, 94, null, null, 1220269093, 1048518583, 1068311203, 1219299559, 1626460, "SRX25380701", "SRS22046053", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.93188, 0.93167, 0.1413, 0.13958, 0.70814, 0.70875, 0.52962, 0.53051, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33285, "SRR29884418", "SRX25380700", "SRS22046052", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Male 4", "GSM8406310", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Male 4", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406310", "GSM8406310: Brain WT Male 4; Danio rerio; RNA Seq", "GSM8406310 r1", "GSM8406310", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample9WTMaleBrain_R1.fastq Sample9WTMaleBrain_R2.fastq", "fastq fastq", 5130577372.0, 26157026.0, "GSM8406310 r1", "0:98.07 1:98.07", "A:1409899035;C:1143333235;G:1163465644;T:1412102322;N:1777136", 98, 98, null, null, 1409899035, 1143333235, 1163465644, 1412102322, 1777136, "SRX25380700", "SRS22046052", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94388, 0.94533, 0.13794, 0.13603, 0.69907, 0.69867, 0.52585, 0.51928, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33286, "SRR29884419", "SRX25380699", "SRS22046054", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Male 3", "GSM8406309", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Male 3", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406309", "GSM8406309: Brain WT Male 3; Danio rerio; RNA Seq", "GSM8406309 r1", "GSM8406309", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample8WTMaleBrain_R1.fastq Sample8WTMaleBrain_R2.fastq", "fastq fastq", 7972815402.0, 40447690.0, "GSM8406309 r1", "0:98.56 1:98.56", "A:2168632819;C:1797135023;G:1834247957;T:2170022014;N:2777589", 98, 98, null, null, 2168632819, 1797135023, 1834247957, 2170022014, 2777589, "SRX25380699", "SRS22046054", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94357, 0.94705, 0.13542, 0.13436, 0.69915, 0.69863, 0.52491, 0.53063, 81, 81, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33287, "SRR29884420", "SRX25380698", "SRS22046051", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Male 2", "GSM8406308", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Male 2", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406308", "GSM8406308: Brain WT Male 2; Danio rerio; RNA Seq", "GSM8406308 r1", "GSM8406308", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample7WTMaleBrain_R1.fastq Sample7WTMaleBrain_R2.fastq", "fastq fastq", 7049713238.0, 35734267.0, "GSM8406308 r1", "0:98.64 1:98.64", "A:1906626428;C:1601451933;G:1627879106;T:1911302856;N:2452915", 98, 98, null, null, 1906626428, 1601451933, 1627879106, 1911302856, 2452915, "SRX25380698", "SRS22046051", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.9436, 0.94611, 0.15189, 0.14982, 0.70272, 0.70293, 0.54976, 0.55028, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33288, "SRR29884421", "SRX25380697", "SRS22046050", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Male 1", "GSM8406307", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Male 1", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406307", "GSM8406307: Brain WT Male 1; Danio rerio; RNA Seq", "GSM8406307 r1", "GSM8406307", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample6WTMaleBrain_R1.fastq Sample6WTMaleBrain_R2.fastq", "fastq fastq", 5957369076.0, 30406342.0, "GSM8406307 r1", "0:97.96 1:97.96", "A:1609314070;C:1357455510;G:1376051649;T:1612447643;N:2100204", 97, 97, null, null, 1609314070, 1357455510, 1376051649, 1612447643, 2100204, "SRX25380697", "SRS22046050", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94515, 0.94596, 0.13859, 0.13741, 0.69459, 0.69386, 0.5113, 0.50829, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33289, "SRR29884422", "SRX25380696", "SRS22046048", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Female 5", "GSM8406306", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Female 5", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406306", "GSM8406306: Brain WT Female 5; Danio rerio; RNA Seq", "GSM8406306 r1", "GSM8406306", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample5WTFemaleBrain_R1.fastq Sample5WTFemaleBrain_R2.fastq", "fastq fastq", 6253800764.0, 31754862.0, "GSM8406306 r1", "0:98.47 1:98.47", "A:1706349321;C:1408396210;G:1425535859;T:1711348232;N:2171142", 98, 98, null, null, 1706349321, 1408396210, 1425535859, 1711348232, 2171142, "SRX25380696", "SRS22046048", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94054, 0.9433, 0.13645, 0.13468, 0.69351, 0.69268, 0.50849, 0.50886, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33290, "SRR29884423", "SRX25380695", "SRS22046047", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Female 4", "GSM8406305", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Female 4", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406305", "GSM8406305: Brain WT Female 4; Danio rerio; RNA Seq", "GSM8406305 r1", "GSM8406305", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample4WTFemaleBrain_R1.fastq Sample4WTFemaleBrain_R2.fastq", "fastq fastq", 6326747176.0, 32181924.0, "GSM8406305 r1", "0:98.30 1:98.30", "A:1726705163;C:1423533467;G:1441282364;T:1733022638;N:2203544", 98, 98, null, null, 1726705163, 1423533467, 1441282364, 1733022638, 2203544, "SRX25380695", "SRS22046047", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94564, 0.9463, 0.13279, 0.13015, 0.69329, 0.69264, 0.52131, 0.52995, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33291, "SRR29884424", "SRX25380694", "SRS22046049", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Female 3", "GSM8406304", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Female 3", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406304", "GSM8406304: Brain WT Female 3; Danio rerio; RNA Seq", "GSM8406304 r1", "GSM8406304", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample3WTFemaleBrain_R1.fastq Sample3WTFemaleBrain_R2.fastq", "fastq fastq", 6158432042.0, 31268580.0, "GSM8406304 r1", "0:98.48 1:98.48", "A:1663143400;C:1401049481;G:1427904493;T:1664192587;N:2142081", 98, 98, null, null, 1663143400, 1401049481, 1427904493, 1664192587, 2142081, "SRX25380694", "SRS22046049", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94243, 0.94497, 0.13191, 0.13006, 0.68454, 0.68335, 0.53268, 0.53362, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33292, "SRR29884425", "SRX25380693", "SRS22046046", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Female 2", "GSM8406303", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Female 2", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406303", "GSM8406303: Brain WT Female 2; Danio rerio; RNA Seq", "GSM8406303 r1", "GSM8406303", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample2WTFemaleBrain_R1.fastq Sample2WTFemaleBrain_R2.fastq", "fastq fastq", 5029227086.0, 25468404.0, "GSM8406303 r1", "0:98.73 1:98.73", "A:1373457097;C:1129749557;G:1148614258;T:1375648797;N:1757377", 98, 98, null, null, 1373457097, 1129749557, 1148614258, 1375648797, 1757377, "SRX25380693", "SRS22046046", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94244, 0.94484, 0.14143, 0.13943, 0.69414, 0.69292, 0.52985, 0.53107, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33293, "SRR29884426", "SRX25380692", "SRS22046045", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Female 1", "GSM8406302", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Female 1", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406302", "GSM8406302: Brain WT Female 1; Danio rerio; RNA Seq", "GSM8406302 r1", "GSM8406302", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample1WTFemaleBrain_R1.fastq Sample1WTFemaleBrain_R2.fastq", "fastq fastq", 6137098342.0, 31214791.0, "GSM8406302 r1", "0:98.30 1:98.30", "A:1678153918;C:1372921889;G:1402049594;T:1681827427;N:2145514", 98, 98, null, null, 1678153918, 1372921889, 1402049594, 1681827427, 2145514, "SRX25380692", "SRS22046045", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.93905, 0.94293, 0.14999, 0.14877, 0.69376, 0.69292, 0.52265, 0.5227, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [34264, "SRR31620789", "SRX26985240", "SRS23451898", "SRP549631", "PRJNA1194578", "Tet proteins regulate differentiation potential across retinal cell types", "GSE283588", "Transcriptome Analysis", "Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis\u2013revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq", null, "pubmed:39713311;pubmed:40140485", null, "36hpf dmut replicate 2", "GSM8666793", null, "source name:eye|tissue:eye|age:36|genotype:tet2 / tet3 / |geo loc name:missing|collection date:missing", "36hpf dmut replicate 2", "Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files", "eye", null, "Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.", null, "tissue:eye|age:36|genotype:tet2 / tet3 / ", "GSM8666793", "GSM8666793: 36hpf dmut replicate 2; Danio rerio; RNA Seq", "GSM8666793 r1", "GSM8666793", "1", "Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP549631", null, null, "36-2_DMUT_Library_GRO2554A2_S5_L001_R1_001.fastq.gz 36-2_DMUT_Library_GRO2554A2_S5_L001_R2_001.fastq.gz", "fastq fastq", 78416374900.0, 664545550.0, "GSM8666793 r1", "0:28 1:90", "A:21577013150;C:17939516025;G:19237904562;T:19657905130;N:4036033", 28, 90, null, null, 21577013150, 17939516025, 19237904562, 19657905130, 4036033, "SRX26985240", "SRS23451898", "SRA2028272", "Gross, Ophthalmology, University of Pittsburgh", "Gross, Ophthalmology, University of Pittsburgh", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [34265, "SRR31620790", "SRX26985239", "SRS23451897", "SRP549631", "PRJNA1194578", "Tet proteins regulate differentiation potential across retinal cell types", "GSE283588", "Transcriptome Analysis", "Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis\u2013revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq", null, "pubmed:39713311;pubmed:40140485", null, "36hpf dmut replicate 1", "GSM8666792", null, "source name:eye|tissue:eye|age:36|genotype:tet2 / tet3 / |geo loc name:missing|collection date:missing", "36hpf dmut replicate 1", "Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files", "eye", null, "Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.", null, "tissue:eye|age:36|genotype:tet2 / tet3 / ", "GSM8666792", "GSM8666792: 36hpf dmut replicate 1; Danio rerio; RNA Seq", "GSM8666792 r1", "GSM8666792", "1", "Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP549631", null, null, "36_1DMUT_LIBRARY_GRO2455A6_S8_L001_R1_001.fastq.gz 36_1DMUT_LIBRARY_GRO2455A6_S8_L001_R2_001.fastq.gz", "fastq fastq", 59960371084.0, 508138738.0, "GSM8666792 r1", "0:28 1:90", "A:16529389286;C:13737763948;G:14793638663;T:14896546895;N:3032292", 28, 90, null, null, 16529389286, 13737763948, 14793638663, 14896546895, 3032292, "SRX26985239", "SRS23451897", "SRA2028272", "Gross, Ophthalmology, University of Pittsburgh", "Gross, Ophthalmology, University of Pittsburgh", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [34266, "SRR31620791", "SRX26985238", "SRS23451896", "SRP549631", "PRJNA1194578", "Tet proteins regulate differentiation potential across retinal cell types", "GSE283588", "Transcriptome Analysis", "Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis\u2013revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq", null, "pubmed:39713311;pubmed:40140485", null, "36hpf sibCTL replicate 2", "GSM8666791", null, "source name:eye|tissue:eye|age:36|genotype:sibCTL|geo loc name:missing|collection date:missing", "36hpf sibCTL replicate 2", "Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files", "eye", null, "Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.", null, "tissue:eye|age:36|genotype:sibCTL", "GSM8666791", "GSM8666791: 36hpf sibCTL replicate 2; Danio rerio; RNA Seq", "GSM8666791 r1", "GSM8666791", "1", "Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP549631", null, null, "36-2_CTL_Library_GRO2554A1_S1_L001_R1_001.fastq.gz 36-2_CTL_Library_GRO2554A1_S1_L001_R2_001.fastq.gz", "fastq fastq", 75169575046.0, 637030297.0, "GSM8666791 r1", "0:28 1:90", "A:20921408123;C:16872043260;G:18114737773;T:19257530991;N:3854899", 28, 90, null, null, 20921408123, 16872043260, 18114737773, 19257530991, 3854899, "SRX26985238", "SRS23451896", "SRA2028272", "Gross, Ophthalmology, University of Pittsburgh", "Gross, Ophthalmology, University of Pittsburgh", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [34267, "SRR31620792", "SRX26985237", "SRS23451894", "SRP549631", "PRJNA1194578", "Tet proteins regulate differentiation potential across retinal cell types", "GSE283588", "Transcriptome Analysis", "Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis\u2013revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq", null, "pubmed:39713311;pubmed:40140485", null, "36hpf sibCTL replicate 1", "GSM8666790", null, "source name:eye|tissue:eye|age:36|genotype:sibCTL|geo loc name:missing|collection date:missing", "36hpf sibCTL replicate 1", "Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files", "eye", null, "Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.", null, "tissue:eye|age:36|genotype:sibCTL", "GSM8666790", "GSM8666790: 36hpf sibCTL replicate 1; Danio rerio; RNA Seq", "GSM8666790 r1", "GSM8666790", "1", "Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP549631", null, null, "36_1CTL_LIBRARY_GRO2455A5_S4_L001_R1_001.fastq.gz 36_1CTL_LIBRARY_GRO2455A5_S4_L001_R2_001.fastq.gz", "fastq fastq", 70127226422.0, 594298529.0, "GSM8666790 r1", "0:28 1:90", "A:19313304121;C:16059894416;G:17310188720;T:17440239265;N:3599900", 28, 90, null, null, 19313304121, 16059894416, 17310188720, 17440239265, 3599900, "SRX26985237", "SRS23451894", "SRA2028272", "Gross, Ophthalmology, University of Pittsburgh", "Gross, Ophthalmology, University of Pittsburgh", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [34268, "SRR31620793", "SRX26985236", "SRS23451895", "SRP549631", "PRJNA1194578", "Tet proteins regulate differentiation potential across retinal cell types", "GSE283588", "Transcriptome Analysis", "Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis\u2013revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq", null, "pubmed:39713311;pubmed:40140485", null, "48hpf dmut replicate 2", "GSM8666789", null, "source name:eye|tissue:eye|age:48|genotype:tet2 / tet3 / |geo loc name:missing|collection date:missing", "48hpf dmut replicate 2", "Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files", "eye", null, "Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.", null, "tissue:eye|age:48|genotype:tet2 / tet3 / ", "GSM8666789", "GSM8666789: 48hpf dmut replicate 2; Danio rerio; RNA Seq", "GSM8666789 r1", "GSM8666789", "1", "Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP549631", null, null, "D48_2_GRO1775A18_S13_L001_R1_001.fastq.gz D48_2_GRO1775A18_S13_L001_R2_001.fastq.gz", "fastq fastq", 49713593756.0, 421301642.0, "GSM8666789 r1", "0:28 1:90", "A:13764945916;C:11293471135;G:11713999638;T:12938678190;N:2498877", 28, 90, null, null, 13764945916, 11293471135, 11713999638, 12938678190, 2498877, "SRX26985236", "SRS23451895", "SRA2028272", "Gross, Ophthalmology, University of Pittsburgh", "Gross, Ophthalmology, University of Pittsburgh", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [34269, "SRR31620794", "SRX26985235", "SRS23451893", "SRP549631", "PRJNA1194578", "Tet proteins regulate differentiation potential across retinal cell types", "GSE283588", "Transcriptome Analysis", "Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis\u2013revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq", null, "pubmed:39713311;pubmed:40140485", null, "48hpf dmut replicate 1", "GSM8666788", null, "source name:eye|tissue:eye|age:48|genotype:tet2 / tet3 / |geo loc name:missing|collection date:missing", "48hpf dmut replicate 1", "Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files", "eye", null, "Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.", null, "tissue:eye|age:48|genotype:tet2 / tet3 / ", "GSM8666788", "GSM8666788: 48hpf dmut replicate 1; Danio rerio; RNA Seq", "GSM8666788 r1", "GSM8666788", "1", "Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP549631", null, null, "D48_1_GRO1775A16_S6_L001_R1_001.fastq.gz D48_1_GRO1775A16_S6_L001_R2_001.fastq.gz", "fastq fastq", 61017340862.0, 517096109.0, "GSM8666788 r1", "0:28 1:90", "A:16897864299;C:13758942283;G:14653497314;T:15703925956;N:3111010", 28, 90, null, null, 16897864299, 13758942283, 14653497314, 15703925956, 3111010, "SRX26985235", "SRS23451893", "SRA2028272", "Gross, Ophthalmology, University of Pittsburgh", "Gross, Ophthalmology, University of Pittsburgh", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [34270, "SRR31620795", "SRX26985234", "SRS23451891", "SRP549631", "PRJNA1194578", "Tet proteins regulate differentiation potential across retinal cell types", "GSE283588", "Transcriptome Analysis", "Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis\u2013revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq", null, "pubmed:39713311;pubmed:40140485", null, "48hpf sibCTL replicate 2", "GSM8666787", null, "source name:eye|tissue:eye|age:48|genotype:sibCTL|geo loc name:missing|collection date:missing", "48hpf sibCTL replicate 2", "Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files", "eye", null, "Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.", null, "tissue:eye|age:48|genotype:sibCTL", "GSM8666787", "GSM8666787: 48hpf sibCTL replicate 2; Danio rerio; RNA Seq", "GSM8666787 r1", "GSM8666787", "1", "Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP549631", null, null, "C48_2_GRO1775A17_S10_L001_R1_001.fastq.gz C48_2_GRO1775A17_S10_L001_R2_001.fastq.gz", "fastq fastq", 41617041928.0, 352686796.0, "GSM8666787 r1", "0:28 1:90", "A:11784184401;C:9157967637;G:9647105654;T:11025644618;N:2139618", 28, 90, null, null, 11784184401, 9157967637, 9647105654, 11025644618, 2139618, "SRX26985234", "SRS23451891", "SRA2028272", "Gross, Ophthalmology, University of Pittsburgh", "Gross, Ophthalmology, University of Pittsburgh", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [34271, "SRR31620796", "SRX26985233", "SRS23451892", "SRP549631", "PRJNA1194578", "Tet proteins regulate differentiation potential across retinal cell types", "GSE283588", "Transcriptome Analysis", "Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis\u2013revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq", null, "pubmed:39713311;pubmed:40140485", null, "48hpf sibCTL replicate 1", "GSM8666786", null, "source name:eye|tissue:eye|age:48|genotype:sibCTL|geo loc name:missing|collection date:missing", "48hpf sibCTL replicate 1", "Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files", "eye", null, "Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.", null, "tissue:eye|age:48|genotype:sibCTL", "GSM8666786", "GSM8666786: 48hpf sibCTL replicate 1; Danio rerio; RNA Seq", "GSM8666786 r1", "GSM8666786", "1", "Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP549631", null, null, "C48_1_GRO1775A15_S2_L001_R1_001.fastq.gz C48_1_GRO1775A15_S2_L001_R2_001.fastq.gz", "fastq fastq", 54112599182.0, 458581349.0, "GSM8666786 r1", "0:28 1:90", "A:15198773029;C:11981463118;G:12618365415;T:14311218195;N:2779425", 28, 90, null, null, 15198773029, 11981463118, 12618365415, 14311218195, 2779425, "SRX26985233", "SRS23451892", "SRA2028272", "Gross, Ophthalmology, University of Pittsburgh", "Gross, Ophthalmology, University of Pittsburgh", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [42525, "SRR5687196", "SRX2921961", "SRS2287821", "SRP109268", "PRJNA390613", "Transcripts within Rod Photoreceptors of the Zebrafish Retina", "GSE100062", "Transcriptome Analysis", "Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.", null, "pubmed:29422031", null, "GFPneg5 2", "GSM2670727", null, "tissue:Zebrafish retinal cells not rods|cell type:non rod retinal cells|genotype/variation:XOPS:eGFP|cell type:GFP ; FACS sorted non rods from retina", "GFPneg5 2", "Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation", "Zebrafish retinal cells not rods", "Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37\u00b0C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 \u00b5L phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 \u00b5m nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 \u00b5L of the FACS sheath fluid and RNA was immediately extracted.", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.", "cell type:non rod retinal cells|genotype/variation:XOPS:eGFP|cell type:GFP ; FACS sorted non rods from retina", "GSM2670727", "GSM2670727: GFPneg5 2; Danio rerio; RNA Seq", "GSM2670727", null, "1", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "GEO Accession:GSM2670727", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP109268", null, null, "GFPnegaitive5set2_GTGAAA_L001_R1_001.fastq.gz GFPnegaitive5set2_GTGAAA_L001_R2_001.fastq.gz", "fastq fastq", 1952022216.0, 3158612.0, "GSM2670727 r1", "0:309 1:309", "A:607016523;C:396466091;G:392683679;T:555854857;N:1066", 309, 309, null, null, 607016523, 396466091, 392683679, 555854857, 1066, "SRX2921961", "SRS2287821", "SRA574861", "GEO", "Biological Sciences, University of Idaho", 2, 0.68529, 0.70068, 0.12269, 0.12678, 0.84133, 0.856, 0.71177, 0.82957, 309, 309, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-06-15", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [42526, "SRR5687195", "SRX2921960", "SRS2287820", "SRP109268", "PRJNA390613", "Transcripts within Rod Photoreceptors of the Zebrafish Retina", "GSE100062", "Transcriptome Analysis", "Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.", null, "pubmed:29422031", null, "GFPneg2 2", "GSM2670726", null, "tissue:Zebrafish retinal cells not rods|cell type:non rod retinal cells|genotype/variation:XOPS:eGFP|cell type:GFP ; FACS sorted non rods from retina", "GFPneg2 2", "Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation", "Zebrafish retinal cells not rods", "Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37\u00b0C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 \u00b5L phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 \u00b5m nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 \u00b5L of the FACS sheath fluid and RNA was immediately extracted.", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.", "cell type:non rod retinal cells|genotype/variation:XOPS:eGFP|cell type:GFP ; FACS sorted non rods from retina", "GSM2670726", "GSM2670726: GFPneg2 2; Danio rerio; RNA Seq", "GSM2670726", null, "1", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "GEO Accession:GSM2670726", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP109268", null, null, "GFPnegaitive2set2_ATTCCT_L001_R1_001.fastq.gz GFPnegaitive2set2_ATTCCT_L001_R2_001.fastq.gz", "fastq fastq", 1811912964.0, 2931898.0, "GSM2670726 r1", "0:309 1:309", "A:578442167;C:369836482;G:350128044;T:513498823;N:7448", 309, 309, null, null, 578442167, 369836482, 350128044, 513498823, 7448, "SRX2921960", "SRS2287820", "SRA574861", "GEO", "Biological Sciences, University of Idaho", 2, 0.64969, 0.66677, 0.08798, 0.08966, 0.87984, 0.88684, 0.88277, 0.87474, 309, 309, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-06-15", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [42527, "SRR5687194", "SRX2921959", "SRS2287818", "SRP109268", "PRJNA390613", "Transcripts within Rod Photoreceptors of the Zebrafish Retina", "GSE100062", "Transcriptome Analysis", "Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.", null, "pubmed:29422031", null, "GFPneg2", "GSM2670725", null, "tissue:Zebrafish retinal cells not rods|cell type:non rod retinal cells|genotype/variation:XOPS:eGFP|cell type:GFP ; FACS sorted non rods from retina", "GFPneg2", "Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation", "Zebrafish retinal cells not rods", "Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37\u00b0C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 \u00b5L phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 \u00b5m nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 \u00b5L of the FACS sheath fluid and RNA was immediately extracted.", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.", "cell type:non rod retinal cells|genotype/variation:XOPS:eGFP|cell type:GFP ; FACS sorted non rods from retina", "GSM2670725", "GSM2670725: GFPneg2; Danio rerio; RNA Seq", "GSM2670725", null, "1", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "GEO Accession:GSM2670725", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP109268", null, null, "GFPnegaitive2_CAGATC_L001_R1_001.fastq.gz GFPnegaitive2_CAGATC_L001_R2_001.fastq.gz", "fastq fastq", 1718976888.0, 2781516.0, "GSM2670725 r1", "0:309 1:309", "A:529099301;C:352155163;G:350456178;T:487264195;N:2051", 309, 309, null, null, 529099301, 352155163, 350456178, 487264195, 2051, "SRX2921959", "SRS2287818", "SRA574861", "GEO", "Biological Sciences, University of Idaho", 2, 0.71906, 0.72599, 0.20211, 0.20881, 0.77761, 0.79289, 0.65883, 0.66469, 309, 309, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-06-15", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [42528, "SRR5687193", "SRX2921958", "SRS2287817", "SRP109268", "PRJNA390613", "Transcripts within Rod Photoreceptors of the Zebrafish Retina", "GSE100062", "Transcriptome Analysis", "Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.", null, "pubmed:29422031", null, "GFPneg1", "GSM2670724", null, "tissue:Zebrafish retinal cells not rods|cell type:non rod retinal cells|genotype/variation:XOPS:eGFP|cell type:GFP ; FACS sorted non rods from retina", "GFPneg1", "Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation", "Zebrafish retinal cells not rods", "Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37\u00b0C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 \u00b5L phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 \u00b5m nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 \u00b5L of the FACS sheath fluid and RNA was immediately extracted.", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.", "cell type:non rod retinal cells|genotype/variation:XOPS:eGFP|cell type:GFP ; FACS sorted non rods from retina", "GSM2670724", "GSM2670724: GFPneg1; Danio rerio; RNA Seq", "GSM2670724", null, "1", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "GEO Accession:GSM2670724", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP109268", null, null, "GFPnegaitive1_CGATGT_L001_R1_001.fastq.gz GFPnegaitive1_CGATGT_L001_R2_001.fastq.gz", "fastq fastq", 2018776104.0, 3266628.0, "GSM2670724 r1", "0:309 1:309", "A:608896808;C:414729064;G:413070681;T:582077754;N:1797", 309, 309, null, null, 608896808, 414729064, 413070681, 582077754, 1797, "SRX2921958", "SRS2287817", "SRA574861", "GEO", "Biological Sciences, University of Idaho", 2, 0.72164, 0.72585, 0.19987, 0.20795, 0.78196, 0.80505, 0.65069, 0.64958, 309, 309, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-06-15", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [42529, "SRR5687192", "SRX2921957", "SRS2287816", "SRP109268", "PRJNA390613", "Transcripts within Rod Photoreceptors of the Zebrafish Retina", "GSE100062", "Transcriptome Analysis", "Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.", null, "pubmed:29422031", null, "GFPpos5 2", "GSM2670723", null, "tissue:Zebrafish retinal rod photoreceptors|cell type:rod photoreceptors|genotype/variation:XOPS:eGFP|cell type:GFP+; FACS sorted rods", "GFPpos5 2", "Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation", "Zebrafish retinal rod photoreceptors", "Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37\u00b0C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 \u00b5L phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 \u00b5m nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 \u00b5L of the FACS sheath fluid and RNA was immediately extracted.", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.", "cell type:rod photoreceptors|genotype/variation:XOPS:eGFP|cell type:GFP+; FACS sorted rods", "GSM2670723", "GSM2670723: GFPpos5 2; Danio rerio; RNA Seq", "GSM2670723", null, "1", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "GEO Accession:GSM2670723", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP109268", null, null, "GFPpositive5set2_GTCCGC_L001_R1_001.fastq.gz GFPpositive5set2_GTCCGC_L001_R2_001.fastq.gz", "fastq fastq", 1951035888.0, 3157016.0, "GSM2670723 r1", "0:309 1:309", "A:601202476;C:409815484;G:396381725;T:543631225;N:4978", 309, 309, null, null, 601202476, 409815484, 396381725, 543631225, 4978, "SRX2921957", "SRS2287816", "SRA574861", "GEO", "Biological Sciences, University of Idaho", 2, 0.66385, 0.68047, 0.17016, 0.1787, 0.82327, 0.83437, 0.66766, 0.66412, 309, 309, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-06-15", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [42530, "SRR5687191", "SRX2921956", "SRS2287815", "SRP109268", "PRJNA390613", "Transcripts within Rod Photoreceptors of the Zebrafish Retina", "GSE100062", "Transcriptome Analysis", "Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.", null, "pubmed:29422031", null, "GFPpos2 2", "GSM2670722", null, "tissue:Zebrafish retinal rod photoreceptors|cell type:rod photoreceptors|genotype/variation:XOPS:eGFP|cell type:GFP+; FACS sorted rods", "GFPpos2 2", "Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation", "Zebrafish retinal rod photoreceptors", "Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37\u00b0C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 \u00b5L phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 \u00b5m nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 \u00b5L of the FACS sheath fluid and RNA was immediately extracted.", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.", "cell type:rod photoreceptors|genotype/variation:XOPS:eGFP|cell type:GFP+; FACS sorted rods", "GSM2670722", "GSM2670722: GFPpos2 2; Danio rerio; RNA Seq", "GSM2670722", null, "1", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "GEO Accession:GSM2670722", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP109268", null, null, "GFPpositive2set2_ACTGAT_L001_R1_001.fastq.gz GFPpositive2set2_ACTGAT_L001_R2_001.fastq.gz", "fastq fastq", 1756145880.0, 2841660.0, "GSM2670722 r1", "0:309 1:309", "A:564701465;C:354907068;G:340547873;T:495986512;N:2962", 309, 309, null, null, 564701465, 354907068, 340547873, 495986512, 2962, "SRX2921956", "SRS2287815", "SRA574861", "GEO", "Biological Sciences, University of Idaho", 2, 0.57879, 0.59269, 0.16217, 0.16717, 0.85516, 0.86277, 0.7228, 0.72512, 309, 309, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-06-15", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [42531, "SRR5687190", "SRX2921955", "SRS2287814", "SRP109268", "PRJNA390613", "Transcripts within Rod Photoreceptors of the Zebrafish Retina", "GSE100062", "Transcriptome Analysis", "Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.", null, "pubmed:29422031", null, "GFPpos2", "GSM2670721", null, "tissue:Zebrafish retinal rod photoreceptors|cell type:rod photoreceptors|genotype/variation:XOPS:eGFP|cell type:GFP+; FACS sorted rods", "GFPpos2", "Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation", "Zebrafish retinal rod photoreceptors", "Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37\u00b0C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 \u00b5L phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 \u00b5m nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 \u00b5L of the FACS sheath fluid and RNA was immediately extracted.", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.", "cell type:rod photoreceptors|genotype/variation:XOPS:eGFP|cell type:GFP+; FACS sorted rods", "GSM2670721", "GSM2670721: GFPpos2; Danio rerio; RNA Seq", "GSM2670721", null, "1", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "GEO Accession:GSM2670721", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP109268", null, null, "GFPpositive2_CCGTCC_L001_R1_001.fastq.gz GFPpositive2_CCGTCC_L001_R2_001.fastq.gz", "fastq fastq", 1812864684.0, 2933438.0, "GSM2670721 r1", "0:309 1:309", "A:549595811;C:382846743;G:374776217;T:505641489;N:4424", 309, 309, null, null, 549595811, 382846743, 374776217, 505641489, 4424, "SRX2921955", "SRS2287814", "SRA574861", "GEO", "Biological Sciences, University of Idaho", 2, 0.62676, 0.64046, 0.22945, 0.24228, 0.81268, 0.82574, 0.60502, 0.60668, 309, 309, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-06-15", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [42532, "SRR5687189", "SRX2921954", "SRS2287813", "SRP109268", "PRJNA390613", "Transcripts within Rod Photoreceptors of the Zebrafish Retina", "GSE100062", "Transcriptome Analysis", "Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.", null, "pubmed:29422031", null, "GFPpos1", "GSM2670720", null, "tissue:Zebrafish retinal rod photoreceptors|cell type:rod photoreceptors|genotype/variation:XOPS:eGFP|cell type:GFP+; FACS sorted rods", "GFPpos1", "Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation", "Zebrafish retinal rod photoreceptors", "Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37\u00b0C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 \u00b5L phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 \u00b5m nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 \u00b5L of the FACS sheath fluid and RNA was immediately extracted.", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.", "cell type:rod photoreceptors|genotype/variation:XOPS:eGFP|cell type:GFP+; FACS sorted rods", "GSM2670720", "GSM2670720: GFPpos1; Danio rerio; RNA Seq", "GSM2670720", null, "1", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "GEO Accession:GSM2670720", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP109268", null, null, "GFPpositive1_TGACCA_L001_R1_001.fastq.gz GFPpositive1_TGACCA_L001_R2_001.fastq.gz", "fastq fastq", 2150958270.0, 3480515.0, "GSM2670720 r1", "0:309 1:309", "A:654306402;C:442036224;G:437971529;T:616642033;N:2082", 309, 309, null, null, 654306402, 442036224, 437971529, 616642033, 2082, "SRX2921954", "SRS2287813", "SRA574861", "GEO", "Biological Sciences, University of Idaho", 2, 0.65859, 0.66368, 0.295, 0.31011, 0.79324, 0.81454, 0.55325, 0.5597, 309, 309, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-06-15", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [43470, "SRR6888834", "SRX3839384", "SRS3086672", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "P2 right eye Scar", "GSM3065990", null, "tissue:right eye single cells|cas9 injection:protein|FISH id:P2|organ:right eye|sorted plates:1", "P2 right eye Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "right eye single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P2|organ:right eye|sorted plates:1", "GSM3065990", "GSM3065990: P2 right eye Scar; Danio rerio; RNA Seq", "GSM3065990", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM3065990", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P2-Eye-right-p01-Scar_R1.fastq.gz P2-Eye-right-p01-Scar_R2.fastq.gz", "fastq fastq", 39029616.0, 257084.0, "GSM3065990 r1", "0:75.94 1:75.88", "A:7556894;C:11070936;G:13942796;T:6447595;N:11395", 75, 75, null, null, 7556894, 11070936, 13942796, 6447595, 11395, "SRX3839384", "SRS3086672", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00367, 0.00526, 0.00323, 0.00449, 0.9988, 0.99813, 0.31168, 0.32231, 76, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2018-03-23", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [43471, "SRR6888833", "SRX3839383", "SRS3086669", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "P2 left eye Scar", "GSM3065989", null, "tissue:left eye single cells|cas9 injection:protein|FISH id:P2|organ:left eye|sorted plates:1", "P2 left eye Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "left eye single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P2|organ:left eye|sorted plates:1", "GSM3065989", "GSM3065989: P2 left eye Scar; Danio rerio; RNA Seq", "GSM3065989", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM3065989", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P2-Eye-left-p01-Scar_R2.fastq.gz P2-Eye-left-p01-Scar_R1.fastq.gz", "fastq fastq", 38948398.0, 256405.0, "GSM3065989 r1", "0:75.98 1:75.92", "A:7098142;C:11543244;G:14180784;T:6112258;N:13970", 75, 75, null, null, 7098142, 11543244, 14180784, 6112258, 13970, "SRX3839383", "SRS3086669", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00055, 0.00086, 0.00048, 0.00075, 0.99979, 0.99971, 0.63636, 0.375, 75, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2018-03-23", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [43554, "SRR6020372", "SRX3171475", "SRS2501283", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "R3 right eye Trans", "GSM2776970", null, "source name:right eye single cells|cas9 injection:mRNA|FISH id:R3|tissue:right eye|sorted plates:2", "R3 right eye Trans", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "right eye single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R3|tissue:right eye|sorted plates:2", "GSM2776970", "GSM2776970: R3 right eye Trans; Danio rerio; RNA Seq", "GSM2776970", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776970", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R3_right-eye_Trans_p01_R1.fastq.gz R3_right-eye_Trans_p01_R2.fastq.gz", "fastq fastq", 1232363344.0, 8159367.0, "GSM2776970 r1", "0:75.57 1:75.47", "A:358721828;C:215851348;G:306533357;T:351024145;N:232666", 75, 75, null, null, 358721828, 215851348, 306533357, 351024145, 232666, "SRX3171475", "SRS2501283", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.03878, 0.48751, 0.02989, 0.31199, 0.9932, 0.95678, 0.49115, 0.57852, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [43555, "SRR6020373", "SRX3171475", "SRS2501283", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "R3 right eye Trans", "GSM2776970", null, "source name:right eye single cells|cas9 injection:mRNA|FISH id:R3|tissue:right eye|sorted plates:2", "R3 right eye Trans", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "right eye single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R3|tissue:right eye|sorted plates:2", "GSM2776970", "GSM2776970: R3 right eye Trans; Danio rerio; RNA Seq", "GSM2776970", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776970", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R3_right-eye_Trans_p02_R1.fastq.gz R3_right-eye_Trans_p02_R2.fastq.gz", "fastq fastq", 13506918357.0, 89381621.0, "GSM2776970 r2", "0:75.55 1:75.57", "A:4378616211;C:1844732259;G:3577317917;T:3703682555;N:2569415", 75, 75, null, null, 4378616211, 1844732259, 3577317917, 3703682555, 2569415, "SRX3171475", "SRS2501283", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.13968, 0.38495, 0.10884, 0.24752, 0.99393, 0.97179, 0.42155, 0.58172, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [43556, "SRR6020370", "SRX3171474", "SRS2501284", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "R3 right eye Scar", "GSM2776969", null, "source name:right eye single cells|cas9 injection:mRNA|FISH id:R3|tissue:right eye|sorted plates:2", "R3 right eye Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "right eye single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R3|tissue:right eye|sorted plates:2", "GSM2776969", "GSM2776969: R3 right eye Scar; Danio rerio; RNA Seq", "GSM2776969", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776969", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R3_right-eye_Scar_p01_R1.fastq.gz R3_right-eye_Scar_p01_R2.fastq.gz", "fastq fastq", 16402556.0, 107973.0, "GSM2776969 r1", "0:75.98 1:75.94", "A:2913035;C:4716394;G:6012715;T:2757706;N:2706", 75, 75, null, null, 2913035, 4716394, 6012715, 2757706, 2706, "SRX3171474", "SRS2501284", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00031, 0.00215, 0.00027, 0.00065, 0.99995, 0.99941, 0.5, 0.375, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [43557, "SRR6020371", "SRX3171474", "SRS2501284", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "R3 right eye Scar", "GSM2776969", null, "source name:right eye single cells|cas9 injection:mRNA|FISH id:R3|tissue:right eye|sorted plates:2", "R3 right eye Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "right eye single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R3|tissue:right eye|sorted plates:2", "GSM2776969", "GSM2776969: R3 right eye Scar; Danio rerio; RNA Seq", "GSM2776969", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776969", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R3_right-eye_Scar_p02_R1.fastq.gz R3_right-eye_Scar_p02_R2.fastq.gz", "fastq fastq", 9167189.0, 60361.0, "GSM2776969 r2", "0:75.94 1:75.94", "A:1738353;C:2524474;G:3359567;T:1542690;N:2105", 75, 75, null, null, 1738353, 2524474, 3359567, 1542690, 2105, "SRX3171474", "SRS2501284", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00212, 0.01274, 0.00127, 0.00362, 0.99955, 0.99815, 0.27586, 0.42201, 76, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [43558, "SRR6020369", "SRX3171473", "SRS2501282", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "R3 left eye Scar", "GSM2776968", null, "source name:left eye single cells|cas9 injection:mRNA|FISH id:R3|tissue:left eye|sorted plates:1", "R3 left eye Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "left eye single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R3|tissue:left eye|sorted plates:1", "GSM2776968", "GSM2776968: R3 left eye Scar; Danio rerio; RNA Seq", "GSM2776968", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776968", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R3_left-eye_Scar_p01_R1.fastq.gz R3_left-eye_Scar_p01_R2.fastq.gz", "fastq fastq", 3260057.0, 21462.0, "GSM2776968 r1", "0:75.94 1:75.96", "A:576368;C:943970;G:1229076;T:510377;N:266", 75, 75, null, null, 576368, 943970, 1229076, 510377, 266, "SRX3171473", "SRS2501282", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00061, 0.00925, 0.0003, 0.00287, 0.99991, 0.99947, 0.5, 0.62962, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [43605, "SRR6020322", "SRX3171463", "SRS2501272", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "R1 right eye Trans", "GSM2776958", null, "source name:right eye single cells|cas9 injection:mRNA|FISH id:R1|tissue:right eye|sorted plates:1", "R1 right eye Trans", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "right eye single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R1|tissue:right eye|sorted plates:1", "GSM2776958", "GSM2776958: R1 right eye Trans; Danio rerio; RNA Seq", "GSM2776958", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776958", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R1_right-eye_Trans_p01_R1.fastq.gz R1_right-eye_Trans_p01_R2.fastq.gz", "fastq fastq", 5130322003.0, 34025983.0, "GSM2776958 r1", "0:75.43 1:75.35", "A:1849671847;C:731930699;G:648670890;T:1898907330;N:1141237", 75, 75, null, null, 1849671847, 731930699, 648670890, 1898907330, 1141237, "SRX3171463", "SRS2501272", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.2345, 0.49487, 0.17483, 0.32246, 0.9683, 0.91938, 0.50419, 0.54579, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [43606, "SRR6020321", "SRX3171462", "SRS2501271", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "R1 right eye Scar", "GSM2776957", null, "source name:right eye single cells|cas9 injection:mRNA|FISH id:R1|tissue:right eye|sorted plates:1", "R1 right eye Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "right eye single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R1|tissue:right eye|sorted plates:1", "GSM2776957", "GSM2776957: R1 right eye Scar; Danio rerio; RNA Seq", "GSM2776957", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776957", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R1_right-eye_Scar_p01_R1.fastq.gz R1_right-eye_Scar_p01_R2.fastq.gz", "fastq fastq", 51349725.0, 338093.0, "GSM2776957 r1", "0:75.98 1:75.90", "A:9493047;C:14848060;G:18750237;T:8248478;N:9903", 75, 75, null, null, 9493047, 14848060, 18750237, 8248478, 9903, "SRX3171462", "SRS2501271", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00015, 0.00029, 0.00011, 0.00021, 0.99993, 0.99985, 0.66666, 0.57142, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [43611, "SRR6020315", "SRX3171459", "SRS2501268", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "R1 left eye Trans", "GSM2776954", null, "source name:left eye single cells|cas9 injection:mRNA|FISH id:R1|tissue:left eye|sorted plates:2", "R1 left eye Trans", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "left eye single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R1|tissue:left eye|sorted plates:2", "GSM2776954", "GSM2776954: R1 left eye Trans; Danio rerio; RNA Seq", "GSM2776954", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776954", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R1_left-eye_Trans_p01_R1.fastq.gz R1_left-eye_Trans_p01_R2.fastq.gz", "fastq fastq", 1046170155.0, 6918434.0, "GSM2776954 r1", "0:75.69 1:75.52", "A:295576695;C:221931427;G:229805854;T:298632621;N:223558", 75, 75, null, null, 295576695, 221931427, 229805854, 298632621, 223558, "SRX3171459", "SRS2501268", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.06872, 0.17373, 0.05659, 0.12922, 0.9833, 0.95611, 0.46872, 0.54838, 75, 76, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [43612, "SRR6020316", "SRX3171459", "SRS2501268", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "R1 left eye Trans", "GSM2776954", null, "source name:left eye single cells|cas9 injection:mRNA|FISH id:R1|tissue:left eye|sorted plates:2", "R1 left eye Trans", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "left eye single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R1|tissue:left eye|sorted plates:2", "GSM2776954", "GSM2776954: R1 left eye Trans; Danio rerio; RNA Seq", "GSM2776954", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776954", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R1_left-eye_Trans_p02_R2.fastq.gz R1_left-eye_Trans_p02_R1.fastq.gz", "fastq fastq", 25047483725.0, 165912644.0, "GSM2776954 r2", "0:75.59 1:75.38", "A:6912192763;C:5496852975;G:6032128490;T:6600903816;N:5405681", 75, 75, null, null, 6912192763, 5496852975, 6032128490, 6600903816, 5405681, "SRX3171459", "SRS2501268", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.01804, 0.04542, 0.01535, 0.03794, 0.99492, 0.98774, 0.42283, 0.45955, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [43613, "SRR6020313", "SRX3171458", "SRS2501266", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "R1 left eye Scar", "GSM2776953", null, "source name:left eye single cells|cas9 injection:mRNA|FISH id:R1|tissue:left eye|sorted plates:2", "R1 left eye Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "left eye single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R1|tissue:left eye|sorted plates:2", "GSM2776953", "GSM2776953: R1 left eye Scar; Danio rerio; RNA Seq", "GSM2776953", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776953", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R1_left-eye_Scar_p01_R1.fastq.gz R1_left-eye_Scar_p01_R2.fastq.gz", "fastq fastq", 430346860.0, 2834154.0, "GSM2776953 r1", "0:75.96 1:75.88", "A:78839865;C:124580997;G:157976167;T:68821337;N:128494", 75, 75, null, null, 78839865, 124580997, 157976167, 68821337, 128494, "SRX3171458", "SRS2501266", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 9e-05, 1e-05, 5e-05, 0.0, 0.99997, 0.99997, 0.0, 0.0, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [43614, "SRR6020314", "SRX3171458", "SRS2501266", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "R1 left eye Scar", "GSM2776953", null, "source name:left eye single cells|cas9 injection:mRNA|FISH id:R1|tissue:left eye|sorted plates:2", "R1 left eye Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "left eye single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R1|tissue:left eye|sorted plates:2", "GSM2776953", "GSM2776953: R1 left eye Scar; Danio rerio; RNA Seq", "GSM2776953", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776953", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R1_left-eye_Scar_p02_R1.fastq.gz R1_left-eye_Scar_p02_R2.fastq.gz", "fastq fastq", 840951649.0, 5536337.0, "GSM2776953 r2", "0:75.98 1:75.91", "A:151508446;C:241728170;G:312991163;T:134635263;N:88607", 75, 75, null, null, 151508446, 241728170, 312991163, 134635263, 88607, "SRX3171458", "SRS2501266", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 8e-05, 3e-05, 5e-05, 0.0, 0.99997, 0.99993, 0.0, 0.33333, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [43626, "SRR5961764", "SRX3119875", "SRS2454734", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "P1 right eye Scars", "GSM2752198", null, "source name:right eye single cells|cas9 injection:protein|FISH id:P1|tissue:right eye|sorted plates:2", "P1 right eye Scars", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to 1; and extending gap penalty to 0.1. Subsequently we pool scars per cell and by cigar. For each scar library a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next scars were filtered according to their frequency of detection in the full library. For each cell reads are normalized to 100 and scars representing less than 3.5% are removed. Genome build: In scar libraries: eGFP sequence extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern", "right eye single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P1|tissue:right eye|sorted plates:2", "GSM2752198", "GSM2752198: P1 right eye Scars; Danio rerio; RNA Seq", "GSM2752198", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2752198", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P1_right-eye_Scar_p01_R1.fastq.gz P1_right-eye_Scar_p01_R2.fastq.gz", "fastq fastq", 41294204.0, 271740.0, "GSM2752198 r1", "0:75.99 1:75.97", "A:7444211;C:11950093;G:15212116;T:6685156;N:2628", 75, 75, null, null, 7444211, 11950093, 15212116, 6685156, 2628, "SRX3119875", "SRS2454734", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 6e-05, 0.00023, 4e-05, 0.00017, 0.99993, 0.99981, 0.66666, 0.66666, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-08-23", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [43627, "SRR6930577", "SRX3119875", "SRS2454734", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "P1 right eye Scars", "GSM2752198", null, "source name:right eye single cells|cas9 injection:protein|FISH id:P1|tissue:right eye|sorted plates:2", "P1 right eye Scars", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to 1; and extending gap penalty to 0.1. Subsequently we pool scars per cell and by cigar. For each scar library a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next scars were filtered according to their frequency of detection in the full library. For each cell reads are normalized to 100 and scars representing less than 3.5% are removed. Genome build: In scar libraries: eGFP sequence extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern", "right eye single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P1|tissue:right eye|sorted plates:2", "GSM2752198", "GSM2752198: P1 right eye Scars; Danio rerio; RNA Seq", "GSM2752198", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2752198", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P1_right-eye_Scar_p02_R1.fastq.gz P1_right-eye_Scar_p02_R2.fastq.gz", "fastq fastq", 91033438.0, 599208.0, "GSM2752198 r2", "0:75.97 1:75.96", "A:16805120;C:25814395;G:33115601;T:15269609;N:28713", 75, 75, null, null, 16805120, 25814395, 33115601, 15269609, 28713, "SRX3119875", "SRS2454734", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00381, 0.00672, 0.00333, 0.00593, 0.99845, 0.9975, 0.45238, 0.50769, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-08-23", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [43629, "SRR5961762", "SRX3119873", "SRS2454732", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "P1 left eye Scars", "GSM2752196", null, "source name:left eye single cells|cas9 injection:protein|FISH id:P1|tissue:left eye|sorted plates:1", "P1 left eye Scars", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to 1; and extending gap penalty to 0.1. Subsequently we pool scars per cell and by cigar. For each scar library a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next scars were filtered according to their frequency of detection in the full library. For each cell reads are normalized to 100 and scars representing less than 3.5% are removed. Genome build: In scar libraries: eGFP sequence extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern", "left eye single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P1|tissue:left eye|sorted plates:1", "GSM2752196", "GSM2752196: P1 left eye Scars; Danio rerio; RNA Seq", "GSM2752196", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2752196", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P1_left-eye_Scar_p01_R1.fastq.gz P1_left-eye_Scar_p01_R2.fastq.gz", "fastq fastq", 161576029.0, 1063213.0, "GSM2752196 r1", "0:75.98 1:75.99", "A:29049869;C:46414226;G:59509149;T:26592886;N:9899", 75, 75, null, null, 29049869, 46414226, 59509149, 26592886, 9899, "SRX3119873", "SRS2454732", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 1e-05, 2e-05, 0.0, 0.0, 1.0, 0.99995, null, 0.5, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-08-23", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [52168, "SRR18181438", "SRX14328402", "SRS12144033", "SRP194254", "PRJNA540466", "Characterization of the zebrafish cell landscape at single cell resolution", "GSE130487", "Transcriptome Analysis", "Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.", null, "pubmed:34660600", null, "Eye3", "GSM5924276", null, "source name:eye|strain:Tubingen|tissue:eye|genotype:wild type", "Eye3", "Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.", "eye", null, "Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|tissue:eye|genotype:wild type", "GSM5924276", "GSM5924276: Eye3; Danio rerio; RNA Seq", "GSM5924276", null, "1", "Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM5924276", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP194254", null, "assembly:Danio rerio GRCz10|intentional duplicate", "Eye3.bam", "bam", 15432297300.0, 51440991.0, "GSM5924276 r1", "0:150 1:150", "A:4354553670;C:2433124600;G:2447610770;T:6195160523;N:1847737", 150, 150, null, null, 4354553670, 2433124600, 2447610770, 6195160523, 1847737, "SRX14328402", "SRS12144033", "SRA880843", "GEO", "Zhejiang University", 2, 5e-05, 0.60307, 4e-05, 0.06123, 1.0, 0.86265, null, 0.57125, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-03-01", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [52190, "SRR9058957", "SRX5835157", "SRS4761453", "SRP194254", "PRJNA540466", "Characterization of the zebrafish cell landscape at single cell resolution", "GSE130487", "Transcriptome Analysis", "Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.", null, "pubmed:34660600", null, "Eye1", "GSM3768154", null, "source name:eye|strain:Tubingen|genotype/variation:wild type|tissue:eye", "Eye1", "Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.", "eye", null, "Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|genotype/variation:wild type|tissue:eye", "GSM3768154", "GSM3768154: Eye1; Danio rerio; RNA Seq", "GSM3768154", null, "1", "Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM3768154", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X Ten", null, "SRP194254", null, "assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index", "Eye1.bam", "bam", 37155841274.0, 123032587.0, "GSM3768154 r1", "0:151 1:151", "A:9138846228;C:6458258540;G:6507520861;T:15044585234;N:6630411", 151, 151, null, null, 9138846228, 6458258540, 6507520861, 15044585234, 6630411, "SRX5835157", "SRS4761453", "SRA880843", "GEO", "Zhejiang University", 2, 2e-05, 0.84079, 0.0, 0.04869, 0.99997, 0.84167, 0.0, 0.66089, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2019-05-15", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [52207, "SRR8991397", "SRX5770465", "SRS4704574", "SRP194254", "PRJNA540466", "Characterization of the zebrafish cell landscape at single cell resolution", "GSE130487", "Transcriptome Analysis", "Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.", null, "pubmed:34660600", null, "Eye2", "GSM3740950", null, "source name:eye|strain:Tubingen|genotype:wild type|tissue:eye", "Eye2", "The drop seq core computational tool was used for preprocessing of the Microwell seq data. The implementation is described in the Drop seq computational cookbook http://mccarrolllab.org/dropseq/. Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: http://dec2017.archive.ensembl.org/Danio rerio/Info/Index Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.", "eye", null, "Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|genotype:wild type|tissue:eye", "GSM3740950", "GSM3740950: Eye2; Danio rerio; RNA Seq", "GSM3740950", null, "1", "Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM3740950", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X Ten", null, "SRP194254", null, "assembly:Danio rerio GRCz10", "Eye2.bam", "bam", 37560825992.0, 124373596.0, "GSM3740950 r1", "0:151 1:151", "A:9124157397;C:6448456288;G:6525562883;T:15454078654;N:8570770", 151, 151, null, null, 9124157397, 6448456288, 6525562883, 15454078654, 8570770, "SRX5770465", "SRS4704574", "SRA880843", "GEO", "Zhejiang University", 2, 0.0, 0.79235, 0.0, 0.0383, 1.0, 0.84981, null, 0.57745, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2019-04-30", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [53513, "SRR9906847", "SRX6657804", "SRS5218265", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdahN36R2", "GSM4007833", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 2", "zfRNAnmdahN36R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 2", "GSM4007833", "GSM4007833: zfRNAnmdahN36R2; Danio rerio; RNA Seq", "GSM4007833", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-TF4N_S8_R1_001.fastq.gz THoa-TF4N_S8_R2_001.fastq.gz", "fastq fastq", 7928700600.0, 52858004.0, "GSM4007833 r1", "0:75 1:75", "A:2214653986;C:1699850211;G:1809132429;T:2204054149;N:1009825", 75, 75, null, null, 2214653986, 1699850211, 1809132429, 2204054149, 1009825, "SRX6657804", "SRS5218265", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.88014, 0.90383, 0.394, 0.41783, 0.76607, 0.77043, 0.5474, 0.55256, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53514, "SRR9906846", "SRX6657803", "SRS5218264", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdahN36R1", "GSM4007832", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 1", "zfRNAnmdahN36R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 1", "GSM4007832", "GSM4007832: zfRNAnmdahN36R1; Danio rerio; RNA Seq", "GSM4007832", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-TF3N_S7_R1_001.fastq.gz THoa-TF3N_S7_R2_001.fastq.gz", "fastq fastq", 7863596250.0, 52423975.0, "GSM4007832 r1", "0:75 1:75", "A:2245214380;C:1641445245;G:1740385747;T:2235554179;N:996699", 75, 75, null, null, 2245214380, 1641445245, 1740385747, 2235554179, 996699, "SRX6657803", "SRS5218264", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.86899, 0.89643, 0.43639, 0.46473, 0.76631, 0.77086, 0.53259, 0.53462, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53515, "SRR9906845", "SRX6657802", "SRS5218263", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdahN20R2", "GSM4007831", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 2", "zfRNAnmdahN20R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 2", "GSM4007831", "GSM4007831: zfRNAnmdahN20R2; Danio rerio; RNA Seq", "GSM4007831", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-TF2N_S6_R1_001.fastq.gz THoa-TF2N_S6_R2_001.fastq.gz", "fastq fastq", 11221029450.0, 74806863.0, "GSM4007831 r1", "0:75 1:75", "A:3206652122;C:2349148827;G:2475237997;T:3188565893;N:1424611", 75, 75, null, null, 3206652122, 2349148827, 2475237997, 3188565893, 1424611, "SRX6657802", "SRS5218263", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.86571, 0.89458, 0.44089, 0.4703, 0.77163, 0.77573, 0.54887, 0.54576, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53516, "SRR9906844", "SRX6657801", "SRS5218262", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdahN20R1", "GSM4007830", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 1", "zfRNAnmdahN20R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 1", "GSM4007830", "GSM4007830: zfRNAnmdahN20R1; Danio rerio; RNA Seq", "GSM4007830", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-TF1N_S5_R1_001.fastq.gz THoa-TF1N_S5_R2_001.fastq.gz", "fastq fastq", 11263633950.0, 75090893.0, "GSM4007830 r1", "0:75 1:75", "A:3198241763;C:2374935676;G:2514695492;T:3174314457;N:1446562", 75, 75, null, null, 3198241763, 2374935676, 2514695492, 3174314457, 1446562, "SRX6657801", "SRS5218262", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.87624, 0.90304, 0.39909, 0.42417, 0.76984, 0.77376, 0.53406, 0.53718, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53517, "SRR9906843", "SRX6657800", "SRS5218261", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdahP36R2", "GSM4007829", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 2", "zfRNAnmdahP36R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 2", "GSM4007829", "GSM4007829: zfRNAnmdahP36R2; Danio rerio; RNA Seq", "GSM4007829", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-TF4P_S4_R1_001.fastq.gz THoa-TF4P_S4_R2_001.fastq.gz", "fastq fastq", 10599378900.0, 70662526.0, "GSM4007829 r1", "0:75 1:75", "A:2917939167;C:2338922409;G:2472546084;T:2868616483;N:1354757", 75, 75, null, null, 2917939167, 2338922409, 2472546084, 2868616483, 1354757, "SRX6657800", "SRS5218261", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.89693, 0.9159, 0.31259, 0.33022, 0.7371, 0.74182, 0.56412, 0.56559, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53518, "SRR9906842", "SRX6657799", "SRS5218260", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdahP36R1", "GSM4007828", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 1", "zfRNAnmdahP36R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 1", "GSM4007828", "GSM4007828: zfRNAnmdahP36R1; Danio rerio; RNA Seq", "GSM4007828", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-TF3P_S3_R1_001.fastq.gz THoa-TF3P_S3_R2_001.fastq.gz", "fastq fastq", 11034687150.0, 73564581.0, "GSM4007828 r1", "0:75 1:75", "A:2954740084;C:2509220120;G:2662792371;T:2906521814;N:1412761", 75, 75, null, null, 2954740084, 2509220120, 2662792371, 2906521814, 1412761, "SRX6657799", "SRS5218260", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.90866, 0.9253, 0.29649, 0.3138, 0.7419, 0.74793, 0.57845, 0.59013, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53519, "SRR9906841", "SRX6657798", "SRS5218259", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdahP20R2", "GSM4007827", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2", "zfRNAnmdahP20R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2", "GSM4007827", "GSM4007827: zfRNAnmdahP20R2; Danio rerio; RNA Seq", "GSM4007827", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-TF2P_S2_R1_001.fastq.gz THoa-TF2P_S2_R2_001.fastq.gz", "fastq fastq", 10416796950.0, 69445313.0, "GSM4007827 r1", "0:75 1:75", "A:2846027907;C:2324721617;G:2438862539;T:2805866203;N:1318684", 75, 75, null, null, 2846027907, 2324721617, 2438862539, 2805866203, 1318684, "SRX6657798", "SRS5218259", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.89999, 0.92352, 0.30772, 0.32822, 0.74823, 0.75089, 0.5489, 0.55828, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53520, "SRR9906840", "SRX6657797", "SRS5218258", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdahP20R1", "GSM4007826", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 1", "zfRNAnmdahP20R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 1", "GSM4007826", "GSM4007826: zfRNAnmdahP20R1; Danio rerio; RNA Seq", "GSM4007826", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-TF1P_S1_R1_001.fastq.gz THoa-TF1P_S1_R2_001.fastq.gz", "fastq fastq", 11087990850.0, 73919939.0, "GSM4007826 r1", "0:75 1:75", "A:3086331907;C:2414289581;G:2547013161;T:3038947630;N:1408571", 75, 75, null, null, 3086331907, 2414289581, 2547013161, 3038947630, 1408571, "SRX6657797", "SRS5218258", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.89541, 0.9175, 0.30129, 0.32289, 0.7417, 0.74714, 0.55292, 0.55122, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53521, "SRR9906839", "SRX6657796", "SRS5218257", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaN36R2", "GSM4007825", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 2", "zfRNAnmdaN36R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 2", "GSM4007825", "GSM4007825: zfRNAnmdaN36R2; Danio rerio; RNA Seq", "GSM4007825", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF16N_S7_R1_001.fastq.gz THoa-DF16N_S7_R2_001.fastq.gz", "fastq fastq", 7593295650.0, 50621971.0, "GSM4007825 r1", "0:75 1:75", "A:1842742463;C:1931868500;G:2009769570;T:1805690959;N:3224158", 75, 75, null, null, 1842742463, 1931868500, 2009769570, 1805690959, 3224158, "SRX6657796", "SRS5218257", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.93981, 0.95204, 0.24731, 0.26265, 0.81412, 0.81811, 0.67154, 0.67196, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53522, "SRR9906838", "SRX6657795", "SRS5218256", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaN36R1", "GSM4007824", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 1", "zfRNAnmdaN36R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 1", "GSM4007824", "GSM4007824: zfRNAnmdaN36R1; Danio rerio; RNA Seq", "GSM4007824", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF15N_S6_R1_001.fastq.gz THoa-DF15N_S6_R2_001.fastq.gz", "fastq fastq", 7927875450.0, 52852503.0, "GSM4007824 r1", "0:75 1:75", "A:1938512738;C:1988054202;G:2080463145;T:1917497438;N:3347927", 75, 75, null, null, 1938512738, 1988054202, 2080463145, 1917497438, 3347927, "SRX6657795", "SRS5218256", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.93468, 0.94808, 0.25462, 0.27334, 0.81262, 0.81548, 0.6351, 0.66108, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53523, "SRR9906837", "SRX6657794", "SRS5218255", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaN20R2", "GSM4007823", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 2", "zfRNAnmdaN20R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 2", "GSM4007823", "GSM4007823: zfRNAnmdaN20R2; Danio rerio; RNA Seq", "GSM4007823", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "DF29N_S7_R1_001.fastq.gz DF29N_S7_R2_001.fastq.gz", "fastq fastq", 7876840694.0, 52829905.0, "GSM4007823 r1", "0:74.55 1:74.55", "A:2010274884;C:1895760244;G:1963812981;T:2004863879;N:2128706", 74, 74, null, null, 2010274884, 1895760244, 1963812981, 2004863879, 2128706, "SRX6657794", "SRS5218255", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.90858, 0.91979, 0.28522, 0.29978, 0.81742, 0.82104, 0.6582, 0.65941, 74, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53524, "SRR9906836", "SRX6657793", "SRS5218254", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaN20R1", "GSM4007822", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 1", "zfRNAnmdaN20R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 1", "GSM4007822", "GSM4007822: zfRNAnmdaN20R1; Danio rerio; RNA Seq", "GSM4007822", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF13N_S5_R1_001.fastq.gz THoa-DF13N_S5_R2_001.fastq.gz", "fastq fastq", 8003905950.0, 53359373.0, "GSM4007822 r1", "0:75 1:75", "A:1925414212;C:2030985118;G:2137411382;T:1906727349;N:3367889", 75, 75, null, null, 1925414212, 2030985118, 2137411382, 1906727349, 3367889, "SRX6657793", "SRS5218254", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.94476, 0.95272, 0.22584, 0.24304, 0.81404, 0.8186, 0.68349, 0.6811, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53525, "SRR9906835", "SRX6657792", "SRS5218253", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaN10R2", "GSM4007821", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 2", "zfRNAnmdaN10R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 2", "GSM4007821", "GSM4007821: zfRNAnmdaN10R2; Danio rerio; RNA Seq", "GSM4007821", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF12N_S4_R1_001.fastq.gz THoa-DF12N_S4_R2_001.fastq.gz", "fastq fastq", 7571445300.0, 50476302.0, "GSM4007821 r1", "0:75 1:75", "A:1961355978;C:1793618129;G:1874282399;T:1938980874;N:3207920", 75, 75, null, null, 1961355978, 1793618129, 1874282399, 1938980874, 3207920, "SRX6657792", "SRS5218253", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.91789, 0.93655, 0.28528, 0.30489, 0.7989, 0.80079, 0.6136, 0.62523, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53526, "SRR9906834", "SRX6657791", "SRS5218252", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaN10R1", "GSM4007820", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 1", "zfRNAnmdaN10R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 1", "GSM4007820", "GSM4007820: zfRNAnmdaN10R1; Danio rerio; RNA Seq", "GSM4007820", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF11N_S3_R1_001.fastq.gz THoa-DF11N_S3_R2_001.fastq.gz", "fastq fastq", 6515556150.0, 43437041.0, "GSM4007820 r1", "0:75 1:75", "A:1542198255;C:1688374350;G:1771407578;T:1510810367;N:2765600", 75, 75, null, null, 1542198255, 1688374350, 1771407578, 1510810367, 2765600, "SRX6657791", "SRS5218252", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.94732, 0.95644, 0.21363, 0.23778, 0.82698, 0.83019, 0.69676, 0.69466, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53527, "SRR9906833", "SRX6657790", "SRS5218251", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaN04R2", "GSM4007819", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:4hr|replicate:Replicate 2", "zfRNAnmdaN04R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:4hr|replicate:Replicate 2", "GSM4007819", "GSM4007819: zfRNAnmdaN04R2; Danio rerio; RNA Seq", "GSM4007819", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF10N_S2_R1_001.fastq.gz THoa-DF10N_S2_R2_001.fastq.gz", "fastq fastq", 7522510200.0, 50150068.0, "GSM4007819 r1", "0:75 1:75", "A:1828130590;C:1927363004;G:1976726604;T:1787097599;N:3192403", 75, 75, null, null, 1828130590, 1927363004, 1976726604, 1787097599, 3192403, "SRX6657790", "SRS5218251", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.94502, 0.9468, 0.20905, 0.22188, 0.8436, 0.8454, 0.72316, 0.72635, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53528, "SRR9906832", "SRX6657789", "SRS5218250", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaN04R1", "GSM4007818", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:4hr|replicate:Replicate 1", "zfRNAnmdaN04R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:4hr|replicate:Replicate 1", "GSM4007818", "GSM4007818: zfRNAnmdaN04R1; Danio rerio; RNA Seq", "GSM4007818", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF9N_S1_R1_001.fastq.gz THoa-DF9N_S1_R2_001.fastq.gz", "fastq fastq", 7392867750.0, 49285785.0, "GSM4007818 r1", "0:75 1:75", "A:1807364965;C:1871069705;G:1942445368;T:1768857698;N:3130014", 75, 75, null, null, 1807364965, 1871069705, 1942445368, 1768857698, 3130014, "SRX6657789", "SRS5218250", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.93966, 0.94358, 0.23683, 0.25285, 0.81785, 0.82012, 0.67242, 0.69507, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53529, "SRR9906831", "SRX6657788", "SRS5218249", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaP36R2", "GSM4007817", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 2", "zfRNAnmdaP36R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 2", "GSM4007817", "GSM4007817: zfRNAnmdaP36R2; Danio rerio; RNA Seq", "GSM4007817", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF16P_S7_R1_001.fastq.gz THoa-DF16P_S7_R2_001.fastq.gz", "fastq fastq", 6373735248.0, 42722100.0, "GSM4007817 r1", "0:74.59 1:74.60", "A:1515782870;C:1648277663;G:1705206622;T:1501843556;N:2624537", 74, 74, null, null, 1515782870, 1648277663, 1705206622, 1501843556, 2624537, "SRX6657788", "SRS5218249", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.94124, 0.94458, 0.14833, 0.15451, 0.82012, 0.8239, 0.6622, 0.67093, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53530, "SRR9906830", "SRX6657787", "SRS5218248", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaP36R1", "GSM4007816", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 1", "zfRNAnmdaP36R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 1", "GSM4007816", "GSM4007816: zfRNAnmdaP36R1; Danio rerio; RNA Seq", "GSM4007816", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF15P_S6_R1_001.fastq.gz THoa-DF15P_S6_R2_001.fastq.gz", "fastq fastq", 6569582369.0, 44039507.0, "GSM4007816 r1", "0:74.58 1:74.59", "A:1581167169;C:1668076484;G:1734283999;T:1583362809;N:2691908", 74, 74, null, null, 1581167169, 1668076484, 1734283999, 1583362809, 2691908, "SRX6657787", "SRS5218248", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.92986, 0.93029, 0.15525, 0.16583, 0.80825, 0.81172, 0.65632, 0.67275, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53531, "SRR9906829", "SRX6657786", "SRS5218247", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaP20R2R2", "GSM4007815", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2", "zfRNAnmdaP20R2R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2", "GSM4007815", "GSM4007815: zfRNAnmdaP20R2R2; Danio rerio; RNA Seq", "GSM4007815", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF29P-run2_S7_R1_001.fastq.gz THoa-DF29P-run2_S7_R2_001.fastq.gz", "fastq fastq", 4138950900.0, 27593006.0, "GSM4007815 r1", "0:75 1:75", "A:1036118589;C:1022903513;G:1048995320;T:1027851668;N:3081810", 75, 75, null, null, 1036118589, 1022903513, 1048995320, 1027851668, 3081810, "SRX6657786", "SRS5218247", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.94004, 0.94676, 0.14485, 0.14607, 0.80986, 0.8102, 0.6594, 0.60583, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53532, "SRR9906828", "SRX6657785", "SRS5218246", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaP20R2R1", "GSM4007814", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2", "zfRNAnmdaP20R2R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2", "GSM4007814", "GSM4007814: zfRNAnmdaP20R2R1; Danio rerio; RNA Seq", "GSM4007814", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF29P-run1_S7_R1_001.fastq.gz THoa-DF29P-run1_S7_R2_001.fastq.gz", "fastq fastq", 2345611650.0, 15637411.0, "GSM4007814 r1", "0:75 1:75", "A:586100477;C:579733712;G:596500443;T:582730098;N:546920", 75, 75, null, null, 586100477, 579733712, 596500443, 582730098, 546920, "SRX6657785", "SRS5218246", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.93951, 0.94484, 0.14437, 0.14581, 0.80738, 0.80724, 0.66526, 0.58765, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53533, "SRR9906827", "SRX6657784", "SRS5218245", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaP20R1", "GSM4007813", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 1", "zfRNAnmdaP20R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 1", "GSM4007813", "GSM4007813: zfRNAnmdaP20R1; Danio rerio; RNA Seq", "GSM4007813", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF13P_S5_R1_001.fastq.gz THoa-DF13P_S5_R2_001.fastq.gz", "fastq fastq", 7039003072.0, 47187560.0, "GSM4007813 r1", "0:74.58 1:74.59", "A:1712945752;C:1757482359;G:1842953199;T:1722863594;N:2758168", 74, 74, null, null, 1712945752, 1757482359, 1842953199, 1722863594, 2758168, "SRX6657784", "SRS5218245", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.94233, 0.94816, 0.14168, 0.15153, 0.79977, 0.80549, 0.62578, 0.64305, 72, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53534, "SRR9906826", "SRX6657783", "SRS5218244", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaP10R2", "GSM4007812", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:10hr|replicate:Replicate 2", "zfRNAnmdaP10R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:10hr|replicate:Replicate 2", "GSM4007812", "GSM4007812: zfRNAnmdaP10R2; Danio rerio; RNA Seq", "GSM4007812", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF12P_S4_R1_001.fastq.gz THoa-DF12P_S4_R2_001.fastq.gz", "fastq fastq", 5745697684.0, 38525032.0, "GSM4007812 r1", "0:74.57 1:74.57", "A:1416523959;C:1432155681;G:1476691642;T:1417880795;N:2445607", 74, 74, null, null, 1416523959, 1432155681, 1476691642, 1417880795, 2445607, "SRX6657783", "SRS5218244", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.93423, 0.94349, 0.1837, 0.191, 0.81146, 0.81446, 0.64969, 0.65118, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53535, "SRR9906825", "SRX6657782", "SRS5218243", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaP10R1", "GSM4007811", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:10hr|replicate:Replicate 1", "zfRNAnmdaP10R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:10hr|replicate:Replicate 1", "GSM4007811", "GSM4007811: zfRNAnmdaP10R1; Danio rerio; RNA Seq", "GSM4007811", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF11P_S3_R1_001.fastq.gz THoa-DF11P_S3_R2_001.fastq.gz", "fastq fastq", 4687597951.0, 31430998.0, "GSM4007811 r1", "0:74.56 1:74.58", "A:1186920007;C:1133558971;G:1178442772;T:1186839573;N:1836628", 74, 74, null, null, 1186920007, 1133558971, 1178442772, 1186839573, 1836628, "SRX6657782", "SRS5218243", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.93636, 0.94612, 0.16988, 0.17882, 0.80014, 0.80424, 0.63955, 0.63931, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53536, "SRR9906824", "SRX6657781", "SRS5218242", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaP04R2", "GSM4007810", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:4hr|replicate:Replicate 2", "zfRNAnmdaP04R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:4hr|replicate:Replicate 2", "GSM4007810", "GSM4007810: zfRNAnmdaP04R2; Danio rerio; RNA Seq", "GSM4007810", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF10P_S2_R1_001.fastq.gz THoa-DF10P_S2_R2_001.fastq.gz", "fastq fastq", 5482033611.0, 36761528.0, "GSM4007810 r1", "0:74.56 1:74.57", "A:1399163955;C:1327953597;G:1360796447;T:1391846223;N:2273389", 74, 74, null, null, 1399163955, 1327953597, 1360796447, 1391846223, 2273389, "SRX6657781", "SRS5218242", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.86015, 0.87027, 0.18565, 0.19683, 0.83349, 0.83666, 0.62827, 0.63846, 72, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53537, "SRR9906823", "SRX6657780", "SRS5218241", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaP04R1", "GSM4007809", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:4hr|replicate:Replicate 1", "zfRNAnmdaP04R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001 AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:4hr|replicate:Replicate 1", "GSM4007809", "GSM4007809: zfRNAnmdaP04R1; Danio rerio; RNA Seq", "GSM4007809", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF9P_S1_R1_001.fastq.gz THoa-DF9P_S1_R2_001.fastq.gz", "fastq fastq", 21735411065.0, 145822702.0, "GSM4007809 r1", "0:74.54 1:74.51", "A:5770843248;C:4924186554;G:5223386393;T:5808415210;N:8579660", 74, 74, null, null, 5770843248, 4924186554, 5223386393, 5808415210, 8579660, "SRX6657780", "SRS5218241", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.32804, 0.332, 0.08428, 0.08869, 0.87584, 0.87969, 0.63905, 0.65793, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53538, "SRR9906822", "SRX6657779", "SRS5218240", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAldtN36R2", "GSM4007808", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 2", "zfRNAldtN36R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 2", "GSM4007808", "GSM4007808: zfRNAldtN36R2; Danio rerio; RNA Seq", "GSM4007808", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF8N_S9_R1_001.fastq.gz THoa-DF8N_S9_R2_001.fastq.gz", "fastq fastq", 7461557400.0, 49743716.0, "GSM4007808 r1", "0:75 1:75", "A:1829397197;C:1872660811;G:1943038567;T:1813306644;N:3154181", 75, 75, null, null, 1829397197, 1872660811, 1943038567, 1813306644, 3154181, "SRX6657779", "SRS5218240", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.9181, 0.93155, 0.26114, 0.27679, 0.80152, 0.8045, 0.67335, 0.67474, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53539, "SRR9906821", "SRX6657778", "SRS5218239", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAldtN36R1", "GSM4007807", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 1", "zfRNAldtN36R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 1", "GSM4007807", "GSM4007807: zfRNAldtN36R1; Danio rerio; RNA Seq", "GSM4007807", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF7N_S8_R1_001.fastq.gz THoa-DF7N_S8_R2_001.fastq.gz", "fastq fastq", 7310480700.0, 48736538.0, "GSM4007807 r1", "0:75 1:75", "A:1851060267;C:1761439990;G:1858394380;T:1836486630;N:3099433", 75, 75, null, null, 1851060267, 1761439990, 1858394380, 1836486630, 3099433, "SRX6657778", "SRS5218239", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.92044, 0.93499, 0.28396, 0.29825, 0.77948, 0.7825, 0.62758, 0.63403, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53540, "SRR9906820", "SRX6657777", "SRS5218238", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAldtN20R2", "GSM4007806", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 2", "zfRNAldtN20R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 2", "GSM4007806", "GSM4007806: zfRNAldtN20R2; Danio rerio; RNA Seq", "GSM4007806", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF6N_S9_R1_001.fastq.gz THoa-DF6N_S9_R2_001.fastq.gz", "fastq fastq", 7098730131.0, 47579801.0, "GSM4007806 r1", "0:74.60 1:74.59", "A:1717050162;C:1797575844;G:1860363186;T:1720884708;N:2856231", 74, 74, null, null, 1717050162, 1797575844, 1860363186, 1720884708, 2856231, "SRX6657777", "SRS5218238", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.93627, 0.93912, 0.23916, 0.25175, 0.80945, 0.81418, 0.67342, 0.68259, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53541, "SRR9906819", "SRX6657776", "SRS5218237", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAldtN20R1", "GSM4007805", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 1", "zfRNAldtN20R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 1", "GSM4007805", "GSM4007805: zfRNAldtN20R1; Danio rerio; RNA Seq", "GSM4007805", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF5N_S8_R1_001.fastq.gz THoa-DF5N_S8_R2_001.fastq.gz", "fastq fastq", 7507942092.0, 50334342.0, "GSM4007805 r1", "0:74.59 1:74.57", "A:1866081920;C:1827112880;G:1922774342;T:1888960357;N:3012593", 74, 74, null, null, 1866081920, 1827112880, 1922774342, 1888960357, 3012593, "SRX6657776", "SRS5218237", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.92572, 0.93469, 0.27326, 0.28815, 0.79084, 0.79707, 0.61558, 0.63121, 75, 74, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53542, "SRR9906818", "SRX6657775", "SRS5218236", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAldtN10R2", "GSM4007804", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 2", "zfRNAldtN10R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 2", "GSM4007804", "GSM4007804: zfRNAldtN10R2; Danio rerio; RNA Seq", "GSM4007804", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF4N_S4_R1_001.fastq.gz THoa-DF4N_S4_R2_001.fastq.gz", "fastq fastq", 9118674847.0, 60348350.0, "GSM4007804 r1", "0:75.55 1:75.55", "A:2354247285;C:2165731401;G:2244032848;T:2353621167;N:1042146", 75, 75, null, null, 2354247285, 2165731401, 2244032848, 2353621167, 1042146, "SRX6657775", "SRS5218236", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.90175, 0.91595, 0.25813, 0.27158, 0.79125, 0.7931, 0.62118, 0.61894, 76, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53543, "SRR9906817", "SRX6657774", "SRS5218235", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAldtN10R1R2", "GSM4007803", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 1", "zfRNAldtN10R1R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 1", "GSM4007803", "GSM4007803: zfRNAldtN10R1R2; Danio rerio; RNA Seq", "GSM4007803", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF2N_S4_R1_001.fastq.gz THoa-DF2N_S4_R2_001.fastq.gz", "fastq fastq", 6920389304.0, 45528877.0, "GSM4007803 r1", "0:76 1:76", "A:1832467265;C:1590107325;G:1661000950;T:1836680423;N:133341", 76, 76, null, null, 1832467265, 1590107325, 1661000950, 1836680423, 133341, "SRX6657774", "SRS5218235", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.89667, 0.91615, 0.32531, 0.34748, 0.78407, 0.78628, 0.61109, 0.59996, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53544, "SRR9906816", "SRX6657773", "SRS5218234", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAldtN10R1R1", "GSM4007802", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 1", "zfRNAldtN10R1R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 1", "GSM4007802", "GSM4007802: zfRNAldtN10R1R1; Danio rerio; RNA Seq", "GSM4007802", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "DF2N_S4_R1_001.fastq.gz DF2N_S4_R2_001.fastq.gz", "fastq fastq", 6701567912.0, 44400966.0, "GSM4007802 r1", "0:75.49 1:75.44", "A:1688384411;C:1625844846;G:1698926520;T:1686384951;N:2027184", 75, 75, null, null, 1688384411, 1625844846, 1698926520, 1686384951, 2027184, "SRX6657773", "SRS5218234", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.91379, 0.93036, 0.29573, 0.31837, 0.80034, 0.8017, 0.638, 0.65469, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53545, "SRR9906815", "SRX6657772", "SRS5218233", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAldtN04R2", "GSM4007801", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP |time:4hr|replicate:Replicate 2", "zfRNAldtN04R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP |time:4hr|replicate:Replicate 2", "GSM4007801", "GSM4007801: zfRNAldtN04R2; Danio rerio; RNA Seq", "GSM4007801", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF3N_S3_R1_001.fastq.gz THoa-DF3N_S3_R2_001.fastq.gz", "fastq fastq", 9452762624.0, 62556061.0, "GSM4007801 r1", "0:75.55 1:75.56", "A:2418410246;C:2278741513;G:2354276985;T:2400236180;N:1097700", 75, 75, null, null, 2418410246, 2278741513, 2354276985, 2400236180, 1097700, "SRX6657772", "SRS5218233", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.90533, 0.91159, 0.20572, 0.21726, 0.81349, 0.81436, 0.6425, 0.64845, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53546, "SRR9906814", "SRX6657771", "SRS5218232", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAldtN04R1R2", "GSM4007800", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP |time:4hr|replicate:Replicate 1", "zfRNAldtN04R1R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP |time:4hr|replicate:Replicate 1", "GSM4007800", "GSM4007800: zfRNAldtN04R1R2; Danio rerio; RNA Seq", "GSM4007800", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF1N_S3_R1_001.fastq.gz THoa-DF1N_S3_R2_001.fastq.gz", "fastq fastq", 6443366488.0, 42390569.0, "GSM4007800 r1", "0:76 1:76", "A:1668027282;C:1512803937;G:1592154543;T:1670256264;N:124462", 76, 76, null, null, 1668027282, 1512803937, 1592154543, 1670256264, 124462, "SRX6657771", "SRS5218232", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.90685, 0.92348, 0.30206, 0.32259, 0.80016, 0.80156, 0.63847, 0.61929, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53547, "SRR9906813", "SRX6657770", "SRS5218231", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAldtP36R2R2", "GSM4007799", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 2", "zfRNAldtP36R2R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 2", "GSM4007799", "GSM4007799: zfRNAldtP36R2R2; Danio rerio; RNA Seq", "GSM4007799", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF8P_S9_R1_001.fastq.gz THoa-DF8P_S9_R2_001.fastq.gz", "fastq fastq", 6236494032.0, 41029566.0, "GSM4007799 r1", "0:76 1:76", "A:1465414386;C:1634912062;G:1681819477;T:1454230315;N:117792", 76, 76, null, null, 1465414386, 1634912062, 1681819477, 1454230315, 117792, "SRX6657770", "SRS5218231", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.94408, 0.94952, 0.15494, 0.16176, 0.82404, 0.82544, 0.67236, 0.65741, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53548, "SRR9906812", "SRX6657769", "SRS5218230", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAldtP36R1R2", "GSM4007798", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 1", "zfRNAldtP36R1R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 1", "GSM4007798", "GSM4007798: zfRNAldtP36R1R2; Danio rerio; RNA Seq", "GSM4007798", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF7P_S10_R1_001.fastq.gz THoa-DF7P_S10_R2_001.fastq.gz", "fastq fastq", 7484077973.0, 50162298.0, "GSM4007798 r1", "0:74.59 1:74.61", "A:1782486863;C:1922264544;G:1989068688;T:1787280217;N:2977661", 74, 74, null, null, 1782486863, 1922264544, 1989068688, 1787280217, 2977661, "SRX6657769", "SRS5218230", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.95471, 0.95346, 0.15186, 0.1567, 0.80332, 0.80736, 0.64996, 0.66954, 74, 74, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53549, "SRR9906811", "SRX6657768", "SRS5218229", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian but not mammalian vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish chick and mice. This was conducted during glial development following inner and outer retinal injury as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data together with functional analysis of candidate genes identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence gliosis and neurogenic competence. In zebrafish and chick transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models as well as growth factor treatment. In total we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAldtP20R3", "GSM4007797", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2", "zfRNAldtP20R3", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58 50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters nomodel shift 100 extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome start stop name length of peak region strand integer score for display fold change log10pvalue log10qvalue relative summit position to peak start.", "Retina", "For NMDA damage adult mice either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed and retinas were collected at indicated timepoints. For light damage the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc. Waltham MA and set to 2000 lux. To induce death of rods and cones adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes 3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:EGFP]nt11 albino|condition:Light damage|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2", "GSM4007797", "GSM4007797: zfRNAldtP20R3; Danio rerio; RNA Seq", "GSM4007797", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004 Qiagen. Ribosomal RNA was depleted and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619 Illumina. For tagmentation cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006 Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "DF31P_S8_R1_001.fastq.gz DF31P_S8_R2_001.fastq.gz", "fastq fastq", 8153845075.0, 54684638.0, "GSM4007797 r1", "0:74.54 1:74.57", "A:2035354223;C:2023329236;G:2076788826;T:2016246616;N:2126174", 74, 74, null, null, 2035354223, 2023329236, 2076788826, 2016246616, 2126174, "SRX6657768", "SRS5218229", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.93265, 0.94088, 0.15684, 0.16053, 0.80846, 0.81044, 0.67966, 0.68311, 75, 72, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"]], "truncated": false, 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"run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation_coarse\" = :p0 and \"tissue_curation_coarse\" = :p1 order by rowid limit 101", "params": {"p0": "Multi-stage", "p1": "Sensory System"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 143, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 135, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System&experiment.library_source=TRANSCRIPTOMIC", "selected": false}, {"value": "TRANSCRIPTOMIC SINGLE CELL", "label": "TRANSCRIPTOMIC SINGLE CELL", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System", "results": [{"value": "cDNA", "label": "cDNA", "count": 143, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System&experiment.library_selection=cDNA", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 143, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 143, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System", "results": [{"value": "Multi-stage", "label": "Multi-stage", "count": 143, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?tissue_curation_coarse=Sensory+System", "selected": true}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System", "results": [{"value": "Multi-stage", "label": "Multi-stage", "count": 96, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System&devstage_curation=Multi-stage", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 47, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System&devstage_curation=Undetermined", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System", "results": [{"value": "Sensory System", "label": "Sensory System", "count": 143, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage", "selected": true}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System", "results": [{"value": "Eye", "label": "Eye", "count": 131, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System&tissue_curation=Eye", "selected": false}, {"value": "Lateral Line", "label": "Lateral Line", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System&tissue_curation=Lateral+Line", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System", "results": [{"value": "bulk", "label": "bulk", "count": 57, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System&technology=bulk", "selected": false}, {"value": "unknown", "label": "unknown", "count": 36, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System&technology=unknown", "selected": false}, {"value": "10x", "label": "10x", "count": 19, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System&technology=10x", "selected": false}, {"value": "scartrace", "label": "scartrace", "count": 16, "toggle_url": 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