{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", technology = \"bulk\" and tissue_curation = \"Eye\"", "rows": [[34913, "SRR32335084", "SRX27670022", "SRS24074877", "SRP563805", "PRJNA1223441", "A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression ", "GSE289562", "Transcriptome Analysis", "We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf.  This work will be published as Le et al.  2025: A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression. Heterozygous deletions predicting haploinsufficiency for the Cysteine Rich Motor Neuron 1 CRIM1 gene have been identified in two families with macrophthalmia  colobomatous  with microcornea MACOM  an autosomal dominant trait. Crim1 encodes a type I transmembrane protein that is expressed at the cell membrane of lens epithelial and fiber cells at the stage of lens pit formation. Decreased Crim1 expression in the mouse reduced the number of lens epithelial cells and caused defective adhesion between lens epithelial cells and between the epithelial and fiber cells. We present three patients with heterozygous deletions and truncating variants predicted to result in haploinsufficiency for CRIM1 as further evidence for the role of this gene in eye defects  including retinal coloboma  optic pallor  and glaucoma. We used Clustered Regularly Interspaced Short Palindromic Repeats CRISPR/Cas9 to make a stable Danio rerio model of crim1 deficiency  generating zebrafish that were homozygous for a 2 basepair deletion  c.339 340delCT p.Leu112Leufs*3  in crim1. Homozygous  crim1 /  larvae demonstrated smaller eyes and small and misshapen lenses compared to controls  but we did not observe colobomas. Bulk RNA Seq using dissected eyes from crim1 /  larvae and controls at 72 hpf showed significant downregulation of crim1 and chloride intracellular channel 4 clic4 and upregulation of fibroblast growth factor 1b fgf1b and complement component 1  q subcomponent c1q  amongst other dysregulated genes. Our work strengthens the association between haploinsufficiency for CRIM1 and eye defects and characterizes a stable model of crim1 loss of function for future research. Overall design: We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf. Wildtype and crim1 /  have two replicates.", null, "pubmed:40114969", null, "crim1 knockdown whole eyes  72 hpf  sample 3", "GSM8794307", null, "source name:Whole eye|tissue:Whole eye|cell type:All|genotype:crim1 / |geo loc name:missing|collection date:missing", "crim1 knockdown whole eyes  72 hpf  sample 3", "The quality of raw single end reads of RNA Seq dataset was tested by FastQC http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/ to evaluate the per base sequence quality  quality scores  sequence length distribution and overrepresented adapter/primer sequences.  post quality control with FastQC  data trimming and clipping was performed using BBDuk and aligned against the zebrafish reference genome GRCz11 using STAR. Alignment results were then assessed to check the quality with Qualimap. RSEM was used to quantify genes. Finally  DESeq2 was used to do the downstream analysis for differentially expressed genes. Statistically significant differentially expressed genes DEGs with log2 fold change greater than \u00b10.5 with an adjusted p value \u22640.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM \u22651 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script. Principal component analysis PCA was performed Assembly: GRCz11 Supplementary files format and content: Excel; Statistically significant differentially expressed genes DEGs with log2 fold change greater than \u00b10.5 with an adjusted p value \u22640.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM \u22651 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script.", "Whole eye", null, "Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed \u2018bulk\u2019 RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation\u00ae RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5\u2032 end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3\u2032 end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.", null, "tissue:Whole eye|cell type:All|genotype:crim1 / ", "GSM8794307", "GSM8794307: crim1 knockdown whole eyes  72 hpf  sample 3; Danio rerio; RNA Seq", "GSM8794307 r1", "GSM8794307", "1", "Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed 'bulk' RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation\u00ae RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5\u2032 end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3\u2032 end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP563805", null, null, "crim1-dpf-3_S15_L002_R1_001.fastq.gz", "fastq", 3331893906.0, 50483241.0, "GSM8794307 r1", "0:66", "A:873905674;C:752237090;G:742087342;T:963442356;N:221444", 66, null, null, null, 873905674, 752237090, 742087342, 963442356, 221444, "SRX27670022", "SRS24074877", null, null, "Cincinnati Children's Hospital Medical Center", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-02-13", "Larval", "Larval", "Eye", "Sensory System"], [34914, "SRR32335085", "SRX27670021", "SRS24074876", "SRP563805", "PRJNA1223441", "A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression ", "GSE289562", "Transcriptome Analysis", "We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf.  This work will be published as Le et al.  2025: A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression. Heterozygous deletions predicting haploinsufficiency for the Cysteine Rich Motor Neuron 1 CRIM1 gene have been identified in two families with macrophthalmia  colobomatous  with microcornea MACOM  an autosomal dominant trait. Crim1 encodes a type I transmembrane protein that is expressed at the cell membrane of lens epithelial and fiber cells at the stage of lens pit formation. Decreased Crim1 expression in the mouse reduced the number of lens epithelial cells and caused defective adhesion between lens epithelial cells and between the epithelial and fiber cells. We present three patients with heterozygous deletions and truncating variants predicted to result in haploinsufficiency for CRIM1 as further evidence for the role of this gene in eye defects  including retinal coloboma  optic pallor  and glaucoma. We used Clustered Regularly Interspaced Short Palindromic Repeats CRISPR/Cas9 to make a stable Danio rerio model of crim1 deficiency  generating zebrafish that were homozygous for a 2 basepair deletion  c.339 340delCT p.Leu112Leufs*3  in crim1. Homozygous  crim1 /  larvae demonstrated smaller eyes and small and misshapen lenses compared to controls  but we did not observe colobomas. Bulk RNA Seq using dissected eyes from crim1 /  larvae and controls at 72 hpf showed significant downregulation of crim1 and chloride intracellular channel 4 clic4 and upregulation of fibroblast growth factor 1b fgf1b and complement component 1  q subcomponent c1q  amongst other dysregulated genes. Our work strengthens the association between haploinsufficiency for CRIM1 and eye defects and characterizes a stable model of crim1 loss of function for future research. Overall design: We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf. Wildtype and crim1 /  have two replicates.", null, "pubmed:40114969", null, "crim1 knockdown whole eyes  72 hpf  sample 2", "GSM8794306", null, "source name:Whole eye|tissue:Whole eye|cell type:All|genotype:crim1 / |geo loc name:missing|collection date:missing", "crim1 knockdown whole eyes  72 hpf  sample 2", "The quality of raw single end reads of RNA Seq dataset was tested by FastQC http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/ to evaluate the per base sequence quality  quality scores  sequence length distribution and overrepresented adapter/primer sequences.  post quality control with FastQC  data trimming and clipping was performed using BBDuk and aligned against the zebrafish reference genome GRCz11 using STAR. Alignment results were then assessed to check the quality with Qualimap. RSEM was used to quantify genes. Finally  DESeq2 was used to do the downstream analysis for differentially expressed genes. Statistically significant differentially expressed genes DEGs with log2 fold change greater than \u00b10.5 with an adjusted p value \u22640.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM \u22651 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script. Principal component analysis PCA was performed Assembly: GRCz11 Supplementary files format and content: Excel; Statistically significant differentially expressed genes DEGs with log2 fold change greater than \u00b10.5 with an adjusted p value \u22640.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM \u22651 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script.", "Whole eye", null, "Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed \u2018bulk\u2019 RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation\u00ae RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5\u2032 end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3\u2032 end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.", null, "tissue:Whole eye|cell type:All|genotype:crim1 / ", "GSM8794306", "GSM8794306: crim1 knockdown whole eyes  72 hpf  sample 2; Danio rerio; RNA Seq", "GSM8794306 r1", "GSM8794306", "1", "Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed 'bulk' RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation\u00ae RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5\u2032 end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3\u2032 end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP563805", null, null, "crim1-dpf-2_S11_L002_R1_001.fastq.gz", "fastq", 3491059044.0, 52894834.0, "GSM8794306 r1", "0:66", "A:907771486;C:794245897;G:783248243;T:1005559302;N:234116", 66, null, null, null, 907771486, 794245897, 783248243, 1005559302, 234116, "SRX27670021", "SRS24074876", null, null, "Cincinnati Children's Hospital Medical Center", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-02-13", "Larval", "Larval", "Eye", "Sensory System"], [34915, "SRR32335086", "SRX27670020", "SRS24074875", "SRP563805", "PRJNA1223441", "A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression ", "GSE289562", "Transcriptome Analysis", "We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf.  This work will be published as Le et al.  2025: A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression. Heterozygous deletions predicting haploinsufficiency for the Cysteine Rich Motor Neuron 1 CRIM1 gene have been identified in two families with macrophthalmia  colobomatous  with microcornea MACOM  an autosomal dominant trait. Crim1 encodes a type I transmembrane protein that is expressed at the cell membrane of lens epithelial and fiber cells at the stage of lens pit formation. Decreased Crim1 expression in the mouse reduced the number of lens epithelial cells and caused defective adhesion between lens epithelial cells and between the epithelial and fiber cells. We present three patients with heterozygous deletions and truncating variants predicted to result in haploinsufficiency for CRIM1 as further evidence for the role of this gene in eye defects  including retinal coloboma  optic pallor  and glaucoma. We used Clustered Regularly Interspaced Short Palindromic Repeats CRISPR/Cas9 to make a stable Danio rerio model of crim1 deficiency  generating zebrafish that were homozygous for a 2 basepair deletion  c.339 340delCT p.Leu112Leufs*3  in crim1. Homozygous  crim1 /  larvae demonstrated smaller eyes and small and misshapen lenses compared to controls  but we did not observe colobomas. Bulk RNA Seq using dissected eyes from crim1 /  larvae and controls at 72 hpf showed significant downregulation of crim1 and chloride intracellular channel 4 clic4 and upregulation of fibroblast growth factor 1b fgf1b and complement component 1  q subcomponent c1q  amongst other dysregulated genes. Our work strengthens the association between haploinsufficiency for CRIM1 and eye defects and characterizes a stable model of crim1 loss of function for future research. Overall design: We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf. Wildtype and crim1 /  have two replicates.", null, "pubmed:40114969", null, "crim1 knockdown whole eyes  72 hpf  sample 1", "GSM8794305", null, "source name:Whole eye|tissue:Whole eye|cell type:All|genotype:crim1 /. |geo loc name:missing|collection date:missing", "crim1 knockdown whole eyes  72 hpf  sample 1", "The quality of raw single end reads of RNA Seq dataset was tested by FastQC http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/ to evaluate the per base sequence quality  quality scores  sequence length distribution and overrepresented adapter/primer sequences.  post quality control with FastQC  data trimming and clipping was performed using BBDuk and aligned against the zebrafish reference genome GRCz11 using STAR. Alignment results were then assessed to check the quality with Qualimap. RSEM was used to quantify genes. Finally  DESeq2 was used to do the downstream analysis for differentially expressed genes. Statistically significant differentially expressed genes DEGs with log2 fold change greater than \u00b10.5 with an adjusted p value \u22640.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM \u22651 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script. Principal component analysis PCA was performed Assembly: GRCz11 Supplementary files format and content: Excel; Statistically significant differentially expressed genes DEGs with log2 fold change greater than \u00b10.5 with an adjusted p value \u22640.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM \u22651 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script.", "Whole eye", null, "Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed \u2018bulk\u2019 RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation\u00ae RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5\u2032 end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3\u2032 end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.", null, "tissue:Whole eye|cell type:All|genotype:crim1 /. ", "GSM8794305", "GSM8794305: crim1 knockdown whole eyes  72 hpf  sample 1; Danio rerio; RNA Seq", "GSM8794305 r1", "GSM8794305", "1", "Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed 'bulk' RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation\u00ae RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5\u2032 end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3\u2032 end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP563805", null, null, "crim1-dpf-1_S16_L003_R1_001.fastq.gz", "fastq", 2751667380.0, 41691930.0, "GSM8794305 r1", "0:66", "A:714065903;C:618520760;G:607652792;T:811160146;N:267779", 66, null, null, null, 714065903, 618520760, 607652792, 811160146, 267779, "SRX27670020", "SRS24074875", null, null, "Cincinnati Children's Hospital Medical Center", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-02-13", "Larval", "Larval", "Eye", "Sensory System"], [34916, "SRR32335087", "SRX27670019", "SRS24074874", "SRP563805", "PRJNA1223441", "A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression ", "GSE289562", "Transcriptome Analysis", "We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf.  This work will be published as Le et al.  2025: A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression. Heterozygous deletions predicting haploinsufficiency for the Cysteine Rich Motor Neuron 1 CRIM1 gene have been identified in two families with macrophthalmia  colobomatous  with microcornea MACOM  an autosomal dominant trait. Crim1 encodes a type I transmembrane protein that is expressed at the cell membrane of lens epithelial and fiber cells at the stage of lens pit formation. Decreased Crim1 expression in the mouse reduced the number of lens epithelial cells and caused defective adhesion between lens epithelial cells and between the epithelial and fiber cells. We present three patients with heterozygous deletions and truncating variants predicted to result in haploinsufficiency for CRIM1 as further evidence for the role of this gene in eye defects  including retinal coloboma  optic pallor  and glaucoma. We used Clustered Regularly Interspaced Short Palindromic Repeats CRISPR/Cas9 to make a stable Danio rerio model of crim1 deficiency  generating zebrafish that were homozygous for a 2 basepair deletion  c.339 340delCT p.Leu112Leufs*3  in crim1. Homozygous  crim1 /  larvae demonstrated smaller eyes and small and misshapen lenses compared to controls  but we did not observe colobomas. Bulk RNA Seq using dissected eyes from crim1 /  larvae and controls at 72 hpf showed significant downregulation of crim1 and chloride intracellular channel 4 clic4 and upregulation of fibroblast growth factor 1b fgf1b and complement component 1  q subcomponent c1q  amongst other dysregulated genes. Our work strengthens the association between haploinsufficiency for CRIM1 and eye defects and characterizes a stable model of crim1 loss of function for future research. Overall design: We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf. Wildtype and crim1 /  have two replicates.", null, "pubmed:40114969", null, "wildtype whole eyes  72 hpf  sample 3", "GSM8794304", null, "source name:Whole eye|tissue:Whole eye|cell type:All|genotype:Wildtype|geo loc name:missing|collection date:missing", "wildtype whole eyes  72 hpf  sample 3", "The quality of raw single end reads of RNA Seq dataset was tested by FastQC http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/ to evaluate the per base sequence quality  quality scores  sequence length distribution and overrepresented adapter/primer sequences.  post quality control with FastQC  data trimming and clipping was performed using BBDuk and aligned against the zebrafish reference genome GRCz11 using STAR. Alignment results were then assessed to check the quality with Qualimap. RSEM was used to quantify genes. Finally  DESeq2 was used to do the downstream analysis for differentially expressed genes. Statistically significant differentially expressed genes DEGs with log2 fold change greater than \u00b10.5 with an adjusted p value \u22640.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM \u22651 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script. Principal component analysis PCA was performed Assembly: GRCz11 Supplementary files format and content: Excel; Statistically significant differentially expressed genes DEGs with log2 fold change greater than \u00b10.5 with an adjusted p value \u22640.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM \u22651 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script.", "Whole eye", null, "Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed \u2018bulk\u2019 RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation\u00ae RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5\u2032 end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3\u2032 end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.", null, "tissue:Whole eye|cell type:All|genotype:Wildtype", "GSM8794304", "GSM8794304: wildtype whole eyes  72 hpf  sample 3; Danio rerio; RNA Seq", "GSM8794304 r1", "GSM8794304", "1", "Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed 'bulk' RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation\u00ae RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5\u2032 end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3\u2032 end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP563805", null, null, "crim1-ctr-3_S12_L002_R1_001.fastq.gz", "fastq", 2881865976.0, 43664636.0, "GSM8794304 r1", "0:66", "A:759373846;C:644323432;G:637932338;T:840046555;N:189805", 66, null, null, null, 759373846, 644323432, 637932338, 840046555, 189805, "SRX27670019", "SRS24074874", null, null, "Cincinnati Children's Hospital Medical Center", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-02-13", "Larval", "Larval", "Eye", "Sensory System"], [34917, "SRR32335088", "SRX27670018", "SRS24074873", "SRP563805", "PRJNA1223441", "A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression ", "GSE289562", "Transcriptome Analysis", "We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf.  This work will be published as Le et al.  2025: A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression. Heterozygous deletions predicting haploinsufficiency for the Cysteine Rich Motor Neuron 1 CRIM1 gene have been identified in two families with macrophthalmia  colobomatous  with microcornea MACOM  an autosomal dominant trait. Crim1 encodes a type I transmembrane protein that is expressed at the cell membrane of lens epithelial and fiber cells at the stage of lens pit formation. Decreased Crim1 expression in the mouse reduced the number of lens epithelial cells and caused defective adhesion between lens epithelial cells and between the epithelial and fiber cells. We present three patients with heterozygous deletions and truncating variants predicted to result in haploinsufficiency for CRIM1 as further evidence for the role of this gene in eye defects  including retinal coloboma  optic pallor  and glaucoma. We used Clustered Regularly Interspaced Short Palindromic Repeats CRISPR/Cas9 to make a stable Danio rerio model of crim1 deficiency  generating zebrafish that were homozygous for a 2 basepair deletion  c.339 340delCT p.Leu112Leufs*3  in crim1. Homozygous  crim1 /  larvae demonstrated smaller eyes and small and misshapen lenses compared to controls  but we did not observe colobomas. Bulk RNA Seq using dissected eyes from crim1 /  larvae and controls at 72 hpf showed significant downregulation of crim1 and chloride intracellular channel 4 clic4 and upregulation of fibroblast growth factor 1b fgf1b and complement component 1  q subcomponent c1q  amongst other dysregulated genes. Our work strengthens the association between haploinsufficiency for CRIM1 and eye defects and characterizes a stable model of crim1 loss of function for future research. Overall design: We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf. Wildtype and crim1 /  have two replicates.", null, "pubmed:40114969", null, "wildtype whole eyes  72 hpf  sample 2", "GSM8794303", null, "source name:Whole eye|tissue:Whole eye|cell type:All|genotype:Wildtype|geo loc name:missing|collection date:missing", "wildtype whole eyes  72 hpf  sample 2", "The quality of raw single end reads of RNA Seq dataset was tested by FastQC http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/ to evaluate the per base sequence quality  quality scores  sequence length distribution and overrepresented adapter/primer sequences.  post quality control with FastQC  data trimming and clipping was performed using BBDuk and aligned against the zebrafish reference genome GRCz11 using STAR. Alignment results were then assessed to check the quality with Qualimap. RSEM was used to quantify genes. Finally  DESeq2 was used to do the downstream analysis for differentially expressed genes. Statistically significant differentially expressed genes DEGs with log2 fold change greater than \u00b10.5 with an adjusted p value \u22640.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM \u22651 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script. Principal component analysis PCA was performed Assembly: GRCz11 Supplementary files format and content: Excel; Statistically significant differentially expressed genes DEGs with log2 fold change greater than \u00b10.5 with an adjusted p value \u22640.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM \u22651 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script.", "Whole eye", null, "Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed \u2018bulk\u2019 RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation\u00ae RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5\u2032 end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3\u2032 end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.", null, "tissue:Whole eye|cell type:All|genotype:Wildtype", "GSM8794303", "GSM8794303: wildtype whole eyes  72 hpf  sample 2; Danio rerio; RNA Seq", "GSM8794303 r1", "GSM8794303", "1", "Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed 'bulk' RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation\u00ae RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5\u2032 end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3\u2032 end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP563805", null, null, "crim1-ctr-2_S20_L003_R1_001.fastq.gz", "fastq", 2380780182.0, 36072427.0, "GSM8794303 r1", "0:66", "A:617266566;C:538355433;G:528639561;T:696293971;N:224651", 66, null, null, null, 617266566, 538355433, 528639561, 696293971, 224651, "SRX27670018", "SRS24074873", null, null, "Cincinnati Children's Hospital Medical Center", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-02-13", "Larval", "Larval", "Eye", "Sensory System"], [34918, "SRR32335089", "SRX27670017", "SRS24074872", "SRP563805", "PRJNA1223441", "A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression ", "GSE289562", "Transcriptome Analysis", "We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf.  This work will be published as Le et al.  2025: A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression. Heterozygous deletions predicting haploinsufficiency for the Cysteine Rich Motor Neuron 1 CRIM1 gene have been identified in two families with macrophthalmia  colobomatous  with microcornea MACOM  an autosomal dominant trait. Crim1 encodes a type I transmembrane protein that is expressed at the cell membrane of lens epithelial and fiber cells at the stage of lens pit formation. Decreased Crim1 expression in the mouse reduced the number of lens epithelial cells and caused defective adhesion between lens epithelial cells and between the epithelial and fiber cells. We present three patients with heterozygous deletions and truncating variants predicted to result in haploinsufficiency for CRIM1 as further evidence for the role of this gene in eye defects  including retinal coloboma  optic pallor  and glaucoma. We used Clustered Regularly Interspaced Short Palindromic Repeats CRISPR/Cas9 to make a stable Danio rerio model of crim1 deficiency  generating zebrafish that were homozygous for a 2 basepair deletion  c.339 340delCT p.Leu112Leufs*3  in crim1. Homozygous  crim1 /  larvae demonstrated smaller eyes and small and misshapen lenses compared to controls  but we did not observe colobomas. Bulk RNA Seq using dissected eyes from crim1 /  larvae and controls at 72 hpf showed significant downregulation of crim1 and chloride intracellular channel 4 clic4 and upregulation of fibroblast growth factor 1b fgf1b and complement component 1  q subcomponent c1q  amongst other dysregulated genes. Our work strengthens the association between haploinsufficiency for CRIM1 and eye defects and characterizes a stable model of crim1 loss of function for future research. Overall design: We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf. Wildtype and crim1 /  have two replicates.", null, "pubmed:40114969", null, "wildtype whole eyes  72 hpf  sample 1", "GSM8794302", null, "source name:Whole eye|tissue:Whole eye|cell type:All|genotype:Wildtype|geo loc name:missing|collection date:missing", "wildtype whole eyes  72 hpf  sample 1", "The quality of raw single end reads of RNA Seq dataset was tested by FastQC http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/ to evaluate the per base sequence quality  quality scores  sequence length distribution and overrepresented adapter/primer sequences.  post quality control with FastQC  data trimming and clipping was performed using BBDuk and aligned against the zebrafish reference genome GRCz11 using STAR. Alignment results were then assessed to check the quality with Qualimap. RSEM was used to quantify genes. Finally  DESeq2 was used to do the downstream analysis for differentially expressed genes. Statistically significant differentially expressed genes DEGs with log2 fold change greater than \u00b10.5 with an adjusted p value \u22640.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM \u22651 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script. Principal component analysis PCA was performed Assembly: GRCz11 Supplementary files format and content: Excel; Statistically significant differentially expressed genes DEGs with log2 fold change greater than \u00b10.5 with an adjusted p value \u22640.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM \u22651 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script.", "Whole eye", null, "Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed \u2018bulk\u2019 RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation\u00ae RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5\u2032 end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3\u2032 end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.", null, "tissue:Whole eye|cell type:All|genotype:Wildtype", "GSM8794302", "GSM8794302: wildtype whole eyes  72 hpf  sample 1; Danio rerio; RNA Seq", "GSM8794302 r1", "GSM8794302", "1", "Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed 'bulk' RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation\u00ae RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5\u2032 end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3\u2032 end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP563805", null, null, "crim1-ctr-1_S17_L003_R1_001.fastq.gz", "fastq", 3007758600.0, 45572100.0, "GSM8794302 r1", "0:66", "A:783035033;C:680405728;G:668894784;T:875142229;N:280826", 66, null, null, null, 783035033, 680405728, 668894784, 875142229, 280826, "SRX27670017", "SRS24074872", null, null, "Cincinnati Children's Hospital Medical Center", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-02-13", "Larval", "Larval", "Eye", "Sensory System"], [60457, "SRR12287401", "SRX8790734", "SRS7059126", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 3", "GSM4681961", null, "source name:36hpf zebrafish eyes|treatment:Torrin|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 3", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "treatment:Torrin|age:36hpf|tissue:eyes", "GSM4681961", "GSM4681961: 36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 3; Danio rerio; RNA Seq", "GSM4681961", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681961", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "Tor_3.fq", "fastq", 611438450.0, 12228769.0, "GSM4681961 r1", "0:50", "A:155737074;C:142979561;G:143702101;T:169019714;N:0", 50, null, null, null, 155737074, 142979561, 143702101, 169019714, 0, "SRX8790734", "SRS7059126", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.96219, null, 0.1228, null, 0.73219, null, 0.50697, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60458, "SRR12287400", "SRX8790733", "SRS7059125", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 2", "GSM4681960", null, "source name:36hpf zebrafish eyes|treatment:Torrin|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 2", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "treatment:Torrin|age:36hpf|tissue:eyes", "GSM4681960", "GSM4681960: 36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 2; Danio rerio; RNA Seq", "GSM4681960", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681960", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "Tor_2.fq", "fastq", 610161700.0, 12203234.0, "GSM4681960 r1", "0:50", "A:153768852;C:143410611;G:145248964;T:167733273;N:0", 50, null, null, null, 153768852, 143410611, 145248964, 167733273, 0, "SRX8790733", "SRS7059125", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.96418, null, 0.12127, null, 0.73521, null, 0.50591, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60459, "SRR12287399", "SRX8790732", "SRS7059124", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 1", "GSM4681959", null, "source name:36hpf zebrafish eyes|treatment:Torrin|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 1", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "treatment:Torrin|age:36hpf|tissue:eyes", "GSM4681959", "GSM4681959: 36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 1; Danio rerio; RNA Seq", "GSM4681959", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681959", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "Tor_1.fq", "fastq", 568616650.0, 11372333.0, "GSM4681959 r1", "0:50", "A:143342391;C:133596830;G:136056983;T:155620446;N:0", 50, null, null, null, 143342391, 133596830, 136056983, 155620446, 0, "SRX8790732", "SRS7059124", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.96423, null, 0.1166, null, 0.73811, null, 0.50869, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60460, "SRR12287398", "SRX8790731", "SRS7059123", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 3", "GSM4681958", null, "source name:36hpf zebrafish eyes|treatment:DMSO control|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 3", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "treatment:DMSO control|age:36hpf|tissue:eyes", "GSM4681958", "GSM4681958: 36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 3; Danio rerio; RNA Seq", "GSM4681958", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681958", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "DMSO_3.fq", "fastq", 710747750.0, 14214955.0, "GSM4681958 r1", "0:50", "A:184360596;C:160789051;G:160903077;T:204668511;N:26515", 50, null, null, null, 184360596, 160789051, 160903077, 204668511, 26515, "SRX8790731", "SRS7059123", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.92693, null, 0.14102, null, 0.74233, null, 0.52477, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60461, "SRR12287397", "SRX8790730", "SRS7059122", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 2", "GSM4681957", null, "source name:36hpf zebrafish eyes|treatment:DMSO control|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 2", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "treatment:DMSO control|age:36hpf|tissue:eyes", "GSM4681957", "GSM4681957: 36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 2; Danio rerio; RNA Seq", "GSM4681957", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681957", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "DMSO_2.fq", "fastq", 710470350.0, 14209407.0, "GSM4681957 r1", "0:50", "A:180578463;C:165554366;G:164357951;T:199952943;N:26627", 50, null, null, null, 180578463, 165554366, 164357951, 199952943, 26627, "SRX8790730", "SRS7059122", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.92993, null, 0.12326, null, 0.73316, null, 0.50795, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60462, "SRR12287396", "SRX8790729", "SRS7059121", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 1", "GSM4681956", null, "source name:36hpf zebrafish eyes|treatment:DMSO control|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 1", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "treatment:DMSO control|age:36hpf|tissue:eyes", "GSM4681956", "GSM4681956: 36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 1; Danio rerio; RNA Seq", "GSM4681956", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681956", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "DMSO_1.fq", "fastq", 684145550.0, 13682911.0, "GSM4681956 r1", "0:50", "A:176031808;C:157711101;G:157012646;T:193364628;N:25367", 50, null, null, null, 176031808, 157711101, 157012646, 193364628, 25367, "SRX8790729", "SRS7059121", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.93134, null, 0.11826, null, 0.73742, null, 0.51639, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60463, "SRR12287395", "SRX8790728", "SRS7059120", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 3", "GSM4681955", null, "source name:36hpf zebrafish eyes|genotype:Wnt2ba overexpression|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 3", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:Wnt2ba overexpression|age:36hpf|tissue:eyes", "GSM4681955", "GSM4681955: 36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 3; Danio rerio; RNA Seq", "GSM4681955", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681955", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "Wnt2b_3.fq", "fastq", 1683174573.0, 33003423.0, "GSM4681955 r1", "0:51", "A:425533518;C:379417030;G:382377050;T:466758495;N:29088480", 51, null, null, null, 425533518, 379417030, 382377050, 466758495, 29088480, "SRX8790728", "SRS7059120", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.92087, null, 0.07926, null, 0.72699, null, 0.50196, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60464, "SRR12287394", "SRX8790727", "SRS7059119", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 2", "GSM4681954", null, "source name:36hpf zebrafish eyes|genotype:Wnt2ba overexpression|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 2", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:Wnt2ba overexpression|age:36hpf|tissue:eyes", "GSM4681954", "GSM4681954: 36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 2; Danio rerio; RNA Seq", "GSM4681954", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681954", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "Wnt2b_2.fq", "fastq", 1491166815.0, 29238565.0, "GSM4681954 r1", "0:51", "A:378958250;C:335771876;G:337239729;T:413432220;N:25764740", 51, null, null, null, 378958250, 335771876, 337239729, 413432220, 25764740, "SRX8790727", "SRS7059119", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.92209, null, 0.08083, null, 0.733, null, 0.51077, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60465, "SRR12287393", "SRX8790726", "SRS7059118", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 1", "GSM4681953", null, "source name:36hpf zebrafish eyes|genotype:Wnt2ba overexpression|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 1", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:Wnt2ba overexpression|age:36hpf|tissue:eyes", "GSM4681953", "GSM4681953: 36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 1; Danio rerio; RNA Seq", "GSM4681953", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681953", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "Wnt2b_1.fq", "fastq", 1919112507.0, 37629657.0, "GSM4681953 r1", "0:51", "A:477418936;C:433410513;G:453965639;T:530637937;N:23679482", 51, null, null, null, 477418936, 433410513, 453965639, 530637937, 23679482, "SRX8790726", "SRS7059118", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.78015, null, 0.06857, null, 0.73608, null, 0.49023, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60466, "SRR12287392", "SRX8790725", "SRS7059117", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "YapS87A  replicate3", "GSM4681952", null, "source name:36hpf zebrafish eyes|genotype:YapS87A overexpression|age:36hpf|tissue:eyes", "YapS87A  replicate3", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:YapS87A overexpression|age:36hpf|tissue:eyes", "GSM4681952", "GSM4681952: YapS87A  replicate3; Danio rerio; RNA Seq", "GSM4681952", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681952", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "YapS87A_3_sequence.txt", "fastq", 1680502581.0, 32951031.0, "GSM4681952 r1", "0:51", "A:431882743;C:376993099;G:378520286;T:464147117;N:28959336", 51, null, null, null, 431882743, 376993099, 378520286, 464147117, 28959336, "SRX8790725", "SRS7059117", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.9063, null, 0.08494, null, 0.73308, null, 0.45344, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60467, "SRR12287391", "SRX8790724", "SRS7059116", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "YapS87A  replicate2", "GSM4681951", null, "source name:36hpf zebrafish eyes|genotype:YapS87A overexpression|age:36hpf|tissue:eyes", "YapS87A  replicate2", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:YapS87A overexpression|age:36hpf|tissue:eyes", "GSM4681951", "GSM4681951: YapS87A  replicate2; Danio rerio; RNA Seq", "GSM4681951", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681951", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "YapS87A_2_sequence.txt", "fastq", 1742004705.0, 34156955.0, "GSM4681951 r1", "0:51", "A:447373634;C:393295480;G:396777263;T:483090843;N:21467485", 51, null, null, null, 447373634, 393295480, 396777263, 483090843, 21467485, "SRX8790724", "SRS7059116", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.90564, null, 0.08572, null, 0.72721, null, 0.46483, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60468, "SRR12287390", "SRX8790723", "SRS7059115", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "YapS87A  replicate1", "GSM4681950", null, "source name:36hpf zebrafish eyes|genotype:YapS87A overexpression|age:36hpf|tissue:eyes", "YapS87A  replicate1", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:YapS87A overexpression|age:36hpf|tissue:eyes", "GSM4681950", "GSM4681950: YapS87A  replicate1; Danio rerio; RNA Seq", "GSM4681950", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681950", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "YapS87A_1_sequence.txt", "fastq", 1605602451.0, 31482401.0, "GSM4681950 r1", "0:51", "A:416296166;C:357147049;G:359581538;T:444847570;N:27730128", 51, null, null, null, 416296166, 357147049, 359581538, 444847570, 27730128, "SRX8790723", "SRS7059115", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.90205, null, 0.08929, null, 0.72949, null, 0.47221, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60469, "SRR12287389", "SRX8790722", "SRS7059114", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate3", "GSM4681949", null, "source name:36hpf zebrafish eyes|genotype:Gal4 Control for Wnt2b and YapS87A|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate3", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:Gal4 Control for Wnt2b and YapS87A|age:36hpf|tissue:eyes", "GSM4681949", "GSM4681949: 36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate3; Danio rerio; RNA Seq", "GSM4681949", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681949", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "WT_3_sequence.txt", "fastq", 1609588305.0, 31560555.0, "GSM4681949 r1", "0:51", "A:412663150;C:358619332;G:364439350;T:446055681;N:27810792", 51, null, null, null, 412663150, 358619332, 364439350, 446055681, 27810792, "SRX8790722", "SRS7059114", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.92187, null, 0.07809, null, 0.73517, null, 0.46998, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60470, "SRR12287388", "SRX8790721", "SRS7059113", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate2", "GSM4681948", null, "source name:36hpf zebrafish eyes|genotype:Gal4 Control for Wnt2b and YapS87A|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate2", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:Gal4 Control for Wnt2b and YapS87A|age:36hpf|tissue:eyes", "GSM4681948", "GSM4681948: 36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate2; Danio rerio; RNA Seq", "GSM4681948", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681948", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "WT_2_sequence.txt", "fastq", 1637145594.0, 32100894.0, "GSM4681948 r1", "0:51", "A:414176151;C:369403072;G:372539483;T:452762354;N:28264534", 51, null, null, null, 414176151, 369403072, 372539483, 452762354, 28264534, "SRX8790721", "SRS7059113", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.92354, null, 0.08166, null, 0.73174, null, 0.47515, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60471, "SRR12287387", "SRX8790720", "SRS7059112", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate1", "GSM4681947", null, "source name:36hpf zebrafish eyes|genotype:Gal4 Control for Wnt2b and YapS87A|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate1", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:Gal4 Control for Wnt2b and YapS87A|age:36hpf|tissue:eyes", "GSM4681947", "GSM4681947: 36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate1; Danio rerio; RNA Seq", "GSM4681947", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681947", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "WT_1_sequence.txt", "fastq", 1666445961.0, 32675411.0, "GSM4681947 r1", "0:51", "A:421437796;C:380026405;G:379400332;T:465027467;N:20553961", 51, null, null, null, 421437796, 380026405, 379400332, 465027467, 20553961, "SRX8790720", "SRS7059112", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.91939, null, 0.07636, null, 0.73052, null, 0.4731, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60472, "SRR12287386", "SRX8790719", "SRS7059111", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 3", "GSM4681946", null, "source name:36hpf zebrafish eyes|genotype:NICD overexpression|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 3", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:NICD overexpression|age:36hpf|tissue:eyes", "GSM4681946", "GSM4681946: 36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 3; Danio rerio; RNA Seq", "GSM4681946", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681946", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "NICD_3.fq", "fastq", 1687493202.0, 33088102.0, "GSM4681946 r1", "0:51", "A:466000780;C:363861781;G:362676818;T:465728464;N:29225359", 51, null, null, null, 466000780, 363861781, 362676818, 465728464, 29225359, "SRX8790719", "SRS7059111", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.90234, null, 0.10242, null, 0.71488, null, 0.47661, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60473, "SRR12287385", "SRX8790718", "SRS7059110", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 2", "GSM4681945", null, "source name:36hpf zebrafish eyes|genotype:NICD overexpression|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 2", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:NICD overexpression|age:36hpf|tissue:eyes", "GSM4681945", "GSM4681945: 36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 2; Danio rerio; RNA Seq", "GSM4681945", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681945", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "NICD_2.fq", "fastq", 1724098248.0, 33805848.0, "GSM4681945 r1", "0:51", "A:479329096;C:373215849;G:370751023;T:475738259;N:25064021", 51, null, null, null, 479329096, 373215849, 370751023, 475738259, 25064021, "SRX8790718", "SRS7059110", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.90041, null, 0.1068, null, 0.71571, null, 0.48007, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60474, "SRR12287384", "SRX8790717", "SRS7059109", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 1", "GSM4681944", null, "source name:36hpf zebrafish eyes|genotype:NICD overexpression|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 1", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:NICD overexpression|age:36hpf|tissue:eyes", "GSM4681944", "GSM4681944: 36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 1; Danio rerio; RNA Seq", "GSM4681944", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681944", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "NICD_1.fq", "fastq", 1929410682.0, 37831582.0, "GSM4681944 r1", "0:51", "A:531140272;C:421394845;G:418288095;T:530541126;N:28046344", 51, null, null, null, 531140272, 421394845, 418288095, 530541126, 28046344, "SRX8790717", "SRS7059109", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.90898, null, 0.10574, null, 0.71898, null, 0.47601, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60475, "SRR12287383", "SRX8790716", "SRS7059108", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 6", "GSM4681943", null, "source name:36hpf zebrafish eyes|genotype:NICD Control|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 6", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:NICD Control|age:36hpf|tissue:eyes", "GSM4681943", "GSM4681943: 36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 6; Danio rerio; RNA Seq", "GSM4681943", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681943", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "NICD_Control_6.fq", "fastq", 2023785927.0, 39682077.0, "GSM4681943 r1", "0:51", "A:561742336;C:444105929;G:439290439;T:558958186;N:19689037", 51, null, null, null, 561742336, 444105929, 439290439, 558958186, 19689037, "SRX8790716", "SRS7059108", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.91779, null, 0.10376, null, 0.72468, null, 0.46199, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60476, "SRR12287382", "SRX8790715", "SRS7059107", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 5", "GSM4681942", null, "source name:36hpf zebrafish eyes|genotype:NICD Control|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 5", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:NICD Control|age:36hpf|tissue:eyes", "GSM4681942", "GSM4681942: 36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 5; Danio rerio; RNA Seq", "GSM4681942", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681942", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "NICD_Control_5.fq", "fastq", 1740124386.0, 34120086.0, "GSM4681942 r1", "0:51", "A:465085934;C:391698178;G:386868685;T:479536883;N:16934706", 51, null, null, null, 465085934, 391698178, 386868685, 479536883, 16934706, "SRX8790715", "SRS7059107", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.92122, null, 0.09508, null, 0.72606, null, 0.47404, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60477, "SRR12287381", "SRX8790714", "SRS7059106", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 1", "GSM4681941", null, "source name:36hpf zebrafish eyes|genotype:NICD Control|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 1", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:NICD Control|age:36hpf|tissue:eyes", "GSM4681941", "GSM4681941: 36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 1; Danio rerio; RNA Seq", "GSM4681941", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681941", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "NICD_Control_1.fq", "fastq", 1876256595.0, 36789345.0, "GSM4681941 r1", "0:51", "A:505568821;C:417420484;G:410313801;T:515696712;N:27256777", 51, null, null, null, 505568821, 417420484, 410313801, 515696712, 27256777, "SRX8790714", "SRS7059106", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.91459, null, 0.09419, null, 0.72512, null, 0.46824, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60478, "SRR12287380", "SRX8790713", "SRS7059105", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 3", "GSM4681940", null, "source name:36hpf zebrafish eyes|genotype:Rab11aDN overexpression|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 3", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:Rab11aDN overexpression|age:36hpf|tissue:eyes", "GSM4681940", "GSM4681940: 36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 3; Danio rerio; RNA Seq", "GSM4681940", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681940", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "Rab11aDN_3.fq", "fastq", 1937833026.0, 37996726.0, "GSM4681940 r1", "0:51", "A:519376884;C:429809002;G:419678420;T:530881829;N:38086891", 51, null, null, null, 519376884, 429809002, 419678420, 530881829, 38086891, "SRX8790713", "SRS7059105", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.9087, null, 0.1008, null, 0.72705, null, 0.47617, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60479, "SRR12287379", "SRX8790712", "SRS7059104", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 2", "GSM4681939", null, "source name:36hpf zebrafish eyes|genotype:Rab11aDN overexpression|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 2", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:Rab11aDN overexpression|age:36hpf|tissue:eyes", "GSM4681939", "GSM4681939: 36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 2; Danio rerio; RNA Seq", "GSM4681939", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681939", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "Rab11aDN_2.fq", "fastq", 1538149392.0, 30159792.0, "GSM4681939 r1", "0:51", "A:404899388;C:344011831;G:336575868;T:422430316;N:30231989", 51, null, null, null, 404899388, 344011831, 336575868, 422430316, 30231989, "SRX8790712", "SRS7059104", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.91044, null, 0.09831, null, 0.72801, null, 0.47546, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60480, "SRR12287378", "SRX8790711", "SRS7059103", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 1", "GSM4681938", null, "source name:36hpf zebrafish eyes|genotype:Rab11aDN overexpression|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 1", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:Rab11aDN overexpression|age:36hpf|tissue:eyes", "GSM4681938", "GSM4681938: 36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 1; Danio rerio; RNA Seq", "GSM4681938", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681938", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "Rab11aDN_1.fq", "fastq", 1642073673.0, 32197523.0, "GSM4681938 r1", "0:51", "A:429811686;C:368457771;G:362183885;T:449347598;N:32272733", 51, null, null, null, 429811686, 368457771, 362183885, 449347598, 32272733, "SRX8790711", "SRS7059103", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.90921, null, 0.09675, null, 0.73133, null, 0.4816, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60481, "SRR12287377", "SRX8790710", "SRS7059102", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 3", "GSM4681937", null, "source name:36hpf zebrafish eyes|genotype:Rab11aDN Control|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 3", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:Rab11aDN Control|age:36hpf|tissue:eyes", "GSM4681937", "GSM4681937: 36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 3; Danio rerio; RNA Seq", "GSM4681937", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681937", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "Rab11aDN_Control_3.fq", "fastq", 1580663604.0, 30993404.0, "GSM4681937 r1", "0:51", "A:412500071;C:356327817;G:348043781;T:432725076;N:31066859", 51, null, null, null, 412500071, 356327817, 348043781, 432725076, 31066859, "SRX8790710", "SRS7059102", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.91358, null, 0.09416, null, 0.72756, null, 0.47659, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60482, "SRR12287376", "SRX8790709", "SRS7059101", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 2", "GSM4681936", null, "source name:36hpf zebrafish eyes|genotype:Rab11aDN Control|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 2", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:Rab11aDN Control|age:36hpf|tissue:eyes", "GSM4681936", "GSM4681936: 36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 2; Danio rerio; RNA Seq", "GSM4681936", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681936", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "Rab11aDN_Control_2.fq", "fastq", 1508085198.0, 29570298.0, "GSM4681936 r1", "0:51", "A:389591011;C:341465324;G:334342859;T:413045227;N:29640777", 51, null, null, null, 389591011, 341465324, 334342859, 413045227, 29640777, "SRX8790709", "SRS7059101", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.91681, null, 0.09096, null, 0.72908, null, 0.47951, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [60483, "SRR12287375", "SRX8790708", "SRS7059100", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 1", "GSM4681935", null, "source name:36hpf zebrafish eyes|genotype:Rab11aDN Control|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 1", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "genotype:Rab11aDN Control|age:36hpf|tissue:eyes", "GSM4681935", "GSM4681935: 36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 1; Danio rerio; RNA Seq", "GSM4681935", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681935", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "Rab11aDN_Control_1.fq", "fastq", 2010222018.0, 39416118.0, "GSM4681935 r1", "0:51", "A:517848834;C:456636261;G:445209526;T:551017897;N:39509500", 51, null, null, null, 517848834, 456636261, 445209526, 551017897, 39509500, "SRX8790708", "SRS7059100", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.91683, null, 0.09045, null, 0.73105, null, 0.4712, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "Pharyngula", "Embryo", "Eye", "Sensory System"], [67683, "SRR17235493", "SRX13414611", "SRS11316492", "SRP350846", "PRJNA789116", "RNAseq of Bbs1 KO Zebrafish larval eyes", "PRJNA789116", "Other", "Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.", null, null, null, null, "BBS1 MUT 10dpf S1", null, "strain:Bbs1ka742|age:10dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype: / |Paired group:D|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larval bbs1 mutant eye", "BBS1 MUT 10dpf S1", "BBS1 MUT 10dpf S1", "TruSeq Stranded Total RNA Library Prep Gold", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350846", null, "fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4", "BBS1_MUT_10dpf_S4_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa", "bam bam", 3635985845.0, 36892654.0, "BBS1 MUT 10dpf S4 merged.bam", "0:98.56", "A:951181543;C:805662797;G:846180468;T:1032919946;N:41091", 98, null, null, null, 951181543, 805662797, 846180468, 1032919946, 41091, "SRX13414611", "SRS11316492", "SRA1343787", "University of Zurich (UZH)|Molecular Life Science", "University of Zurich (UZH)", 1, 0.93818, null, 0.32197, null, 0.69451, null, 0.47394, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "unknown", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2021-12-15", "Larval", "Larval", "Eye", "Sensory System"], [67684, "SRR17235494", "SRX13414610", "SRS11316490", "SRP350846", "PRJNA789116", "RNAseq of Bbs1 KO Zebrafish larval eyes", "PRJNA789116", "Other", "Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.", null, null, null, null, "BBS1 CTRL 10dpf S3", null, "strain:Bbs1ka742|age:10dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype:+/ |Paired group:F|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larval bbs1 mutant eye", "BBS1 CTRL 10dpf S3", "BBS1 CTRL 10dpf S3", "TruSeq Stranded Total RNA Library Prep Gold", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350846", null, "fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4", "BBS1_CTRL_10dpf_S6_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa", "bam bam", 3130875298.0, 31620050.0, "BBS1 CTRL 10dpf S6 merged.bam", "0:99.02", "A:814143728;C:694726254;G:728135378;T:893834285;N:35653", 99, null, null, null, 814143728, 694726254, 728135378, 893834285, 35653, "SRX13414610", "SRS11316490", "SRA1343787", "University of Zurich (UZH)|Molecular Life Science", "University of Zurich (UZH)", 1, 0.94014, null, 0.33329, null, 0.69735, null, 0.47408, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "unknown", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2021-12-15", "Larval", "Larval", "Eye", "Sensory System"], [67685, "SRR17235495", "SRX13414609", "SRS11316491", "SRP350846", "PRJNA789116", "RNAseq of Bbs1 KO Zebrafish larval eyes", "PRJNA789116", "Other", "Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.", null, null, null, null, "BBS1 CTRL 10dpf S2", null, "strain:Bbs1ka742|age:10dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype:+/ |Paired group:E|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larval bbs1 mutant eye", "BBS1 CTRL 10dpf S2", "BBS1 CTRL 10dpf S2", "TruSeq Stranded Total RNA Library Prep Gold", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350846", null, "fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4", "BBS1_CTRL_10dpf_S5_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa", "bam bam", 3062763746.0, 31000736.0, "BBS1 CTRL 10dpf S5 merged.bam", "0:98.80", "A:786649223;C:679725108;G:723425238;T:872929361;N:34816", 98, null, null, null, 786649223, 679725108, 723425238, 872929361, 34816, "SRX13414609", "SRS11316491", "SRA1343787", "University of Zurich (UZH)|Molecular Life Science", "University of Zurich (UZH)", 1, 0.94626, null, 0.26532, null, 0.68793, null, 0.46861, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "unknown", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2021-12-15", "Larval", "Larval", "Eye", "Sensory System"], [67686, "SRR17235496", "SRX13414608", "SRS11316489", "SRP350846", "PRJNA789116", "RNAseq of Bbs1 KO Zebrafish larval eyes", "PRJNA789116", "Other", "Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.", null, null, null, null, "BBS1 Ctrl 10dpf S1", null, "strain:Bbs1ka742|age:10dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype:+/ |Paired group:D|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larval bbs1 mutant eye", "BBS1 Ctrl 10dpf S1", "BBS1 Ctrl 10dpf S1", "TruSeq Stranded Total RNA Library Prep Gold", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350846", null, "fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4", "BBS1_CTRL_10dpf_S4_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa", "bam bam", 4388386557.0, 44385344.0, "BBS1 CTRL 10dpf S4 merged.bam", "0:98.87", "A:1141948730;C:979155774;G:1019331809;T:1247901031;N:49213", 98, null, null, null, 1141948730, 979155774, 1019331809, 1247901031, 49213, "SRX13414608", "SRS11316489", "SRA1343787", "University of Zurich (UZH)|Molecular Life Science", "University of Zurich (UZH)", 1, 0.94326, null, 0.28573, null, 0.69296, null, 0.47244, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "unknown", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2021-12-15", "Larval", "Larval", "Eye", "Sensory System"], [67687, "SRR17235497", "SRX13414607", "SRS11316488", "SRP350846", "PRJNA789116", "RNAseq of Bbs1 KO Zebrafish larval eyes", "PRJNA789116", "Other", "Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.", null, null, null, null, "BBS1 MUT 5dpf S3", null, "strain:Bbs1ka742|age:5dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype: / |Paired group:C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larval bbs1 mutant eye", "BBS1 MUT 5dpf S3", "BBS1 MUT 5dpf S3", "TruSeq Stranded Total RNA Library Prep Gold", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350846", null, "fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4", "BBS1_MUT_5dpf_S3_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa", "bam bam", 3030482374.0, 30617366.0, "BBS1 MUT 5dpf S3 merged.bam", "0:98.98", "A:813926164;C:646079228;G:694857531;T:875585698;N:33753", 98, null, null, null, 813926164, 646079228, 694857531, 875585698, 33753, "SRX13414607", "SRS11316488", "SRA1343787", "University of Zurich (UZH)|Molecular Life Science", "University of Zurich (UZH)", 1, 0.92861, null, 0.41464, null, 0.69051, null, 0.49332, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "unknown", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2021-12-15", "Larval", "Larval", "Eye", "Sensory System"], [67688, "SRR17235498", "SRX13414606", "SRS11316487", "SRP350846", "PRJNA789116", "RNAseq of Bbs1 KO Zebrafish larval eyes", "PRJNA789116", "Other", "Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.", null, null, null, null, "BBS1 MUT 5dpf S2", null, "strain:Bbs1ka742|age:5dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype: / |Paired group:B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larval bbs1 mutant eye", "BBS1 MUT 5dpf S2", "BBS1 MUT 5dpf S2", "TruSeq Stranded Total RNA Library Prep Gold", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350846", null, "fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4", "BBS1_MUT_5dpf_S2_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa", "bam bam", 3714404169.0, 37505417.0, "BBS1 MUT 5dpf S2 merged.bam", "0:99.04", "A:968857332;C:821571707;G:867307403;T:1056625911;N:41816", 99, null, null, null, 968857332, 821571707, 867307403, 1056625911, 41816, "SRX13414606", "SRS11316487", "SRA1343787", "University of Zurich (UZH)|Molecular Life Science", "University of Zurich (UZH)", 1, 0.93912, null, 0.32694, null, 0.68781, null, 0.48549, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "unknown", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2021-12-15", "Larval", "Larval", "Eye", "Sensory System"], [67689, "SRR17235499", "SRX13414605", "SRS11316486", "SRP350846", "PRJNA789116", "RNAseq of Bbs1 KO Zebrafish larval eyes", "PRJNA789116", "Other", "Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.", null, null, null, null, "BBS1 MUT 5dpf S1", null, "strain:Bbs1ka742|age:5dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype: / |Paired group:A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larval bbs1 mutant eye", "BBS1 MUT 5dpf S1", "BBS1 MUT 5dpf S1", "TruSeq Stranded Total RNA Library Prep Gold", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350846", null, "fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4", "BBS1_MUT_5dpf_S1_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa", "bam bam", 3699896449.0, 37382583.0, "BBS1 MUT 5dpf S1 merged.bam", "0:98.97", "A:977907912;C:830475992;G:855441672;T:1036029492;N:41381", 98, null, null, null, 977907912, 830475992, 855441672, 1036029492, 41381, "SRX13414605", "SRS11316486", "SRA1343787", "University of Zurich (UZH)|Molecular Life Science", "University of Zurich (UZH)", 1, 0.93133, null, 0.40806, null, 0.69562, null, 0.5114, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "unknown", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2021-12-15", "Larval", "Larval", "Eye", "Sensory System"], [67690, "SRR17235500", "SRX13414604", "SRS11316485", "SRP350846", "PRJNA789116", "RNAseq of Bbs1 KO Zebrafish larval eyes", "PRJNA789116", "Other", "Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.", null, null, null, null, "BBS1 CTRL 5dpf S3", null, "strain:Bbs1ka742|age:5dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype:+/ |Paired group:C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larval bbs1 mutant eye", "BBS1 CTRL 5dpf S3", "BBS1 CTRL 5dpf S3", "TruSeq Stranded Total RNA Library Prep Gold", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350846", null, "fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4", "BBS1_CTRL_5dpf_S3_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa", "bam bam", 3505192259.0, 35384389.0, "BBS1 CTRL 5dpf S3 merged.bam", "0:99.06", "A:910433958;C:775887812;G:822289434;T:996540997;N:40058", 99, null, null, null, 910433958, 775887812, 822289434, 996540997, 40058, "SRX13414604", "SRS11316485", "SRA1343787", "University of Zurich (UZH)|Molecular Life Science", "University of Zurich (UZH)", 1, 0.94274, null, 0.28843, null, 0.68678, null, 0.47383, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "unknown", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2021-12-15", "Larval", "Larval", "Eye", "Sensory System"], [67691, "SRR17235501", "SRX13414603", "SRS11316483", "SRP350846", "PRJNA789116", "RNAseq of Bbs1 KO Zebrafish larval eyes", "PRJNA789116", "Other", "Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.", null, null, null, null, "BBS1 MUT 10dpf S3", null, "strain:Bbs1ka742|age:10dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype: / |Paired group:F|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larval bbs1 mutant eye", "BBS1 MUT 10dpf S3", "BBS1 MUT 10dpf S3", "TruSeq Stranded Total RNA Library Prep Gold", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350846", null, "fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4", "BBS1_MUT_10dpf_S6_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa", "bam bam", 3821277753.0, 38662066.0, "BBS1 MUT 10dpf S6 merged.bam", "0:98.84", "A:1019329287;C:820362185;G:870436357;T:1111106893;N:43031", 98, null, null, null, 1019329287, 820362185, 870436357, 1111106893, 43031, "SRX13414603", "SRS11316483", "SRA1343787", "University of Zurich (UZH)|Molecular Life Science", "University of Zurich (UZH)", 1, 0.93021, null, 0.40772, null, 0.70019, null, 0.47824, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "unknown", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2021-12-15", "Larval", "Larval", "Eye", "Sensory System"], [67692, "SRR17235502", "SRX13414602", "SRS11316484", "SRP350846", "PRJNA789116", "RNAseq of Bbs1 KO Zebrafish larval eyes", "PRJNA789116", "Other", "Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.", null, null, null, null, "BBS1 MUT 10dpf S2", null, "strain:Bbs1ka742|age:10dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype: / |Paired group:E|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larval bbs1 mutant eye", "BBS1 MUT 10dpf S2", "BBS1 MUT 10dpf S2", "TruSeq Stranded Total RNA Library Prep Gold", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350846", null, "fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4", "BBS1_MUT_10dpf_S5_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa", "bam bam", 2747848263.0, 27781273.0, "BBS1 MUT 10dpf S5 merged.bam", "0:98.91", "A:726140802;C:605265574;G:628347573;T:788063451;N:30863", 98, null, null, null, 726140802, 605265574, 628347573, 788063451, 30863, "SRX13414602", "SRS11316484", "SRA1343787", "University of Zurich (UZH)|Molecular Life Science", "University of Zurich (UZH)", 1, 0.93216, null, 0.39301, null, 0.70009, null, 0.50624, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "unknown", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2021-12-15", "Larval", "Larval", "Eye", "Sensory System"], [67693, "SRR17235503", "SRX13414601", "SRS11316482", "SRP350846", "PRJNA789116", "RNAseq of Bbs1 KO Zebrafish larval eyes", "PRJNA789116", "Other", "Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.", null, null, null, null, "BBS1 CTRL 5dpf S2", null, "strain:Bbs1ka742|age:5dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype:+/ |Paired group:B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larval bbs1 mutant eye", "BBS1 CTRL 5dpf S2", "BBS1 CTRL 5dpf S2", "TruSeq Stranded Total RNA Library Prep Gold", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350846", null, "fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4", "BBS1_CTRL_5dpf_S2_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa", "bam bam", 3371457502.0, 33990750.0, "BBS1 CTRL 5dpf S2 merged.bam", "0:99.19", "A:865249225;C:752466820;G:799272800;T:954431124;N:37533", 99, null, null, null, 865249225, 752466820, 799272800, 954431124, 37533, "SRX13414601", "SRS11316482", "SRA1343787", "University of Zurich (UZH)|Molecular Life Science", "University of Zurich (UZH)", 1, 0.94297, null, 0.30382, null, 0.68523, null, 0.49502, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "unknown", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2021-12-15", "Larval", "Larval", "Eye", "Sensory System"], [67694, "SRR17235504", "SRX13414600", "SRS11316481", "SRP350846", "PRJNA789116", "RNAseq of Bbs1 KO Zebrafish larval eyes", "PRJNA789116", "Other", "Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.", null, null, null, null, "BBS1 CTRL 5dpf S1", null, "strain:Bbs1ka742|age:5dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype:+/ |Paired group:A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: larval bbs1 mutant eye", "BBS1 CTRL 5dpf S1", "BBS1 CTRL 5dpf S1", "TruSeq Stranded Total RNA Library Prep Gold", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350846", null, "fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4", "BBS1_CTRL_5dpf_S1_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa", "bam bam", 3243942424.0, 32951170.0, "BBS1 CTRL 5dpf S1 merged.bam", "0:98.45", "A:886651528;C:694664952;G:729637645;T:932951711;N:36588", 98, null, null, null, 886651528, 694664952, 729637645, 932951711, 36588, "SRX13414600", "SRS11316481", "SRA1343787", "University of Zurich (UZH)|Molecular Life Science", "University of Zurich (UZH)", 1, 0.92662, null, 0.42838, null, 0.69404, null, 0.48808, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "unknown", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2021-12-15", "Larval", "Larval", "Eye", "Sensory System"], [71733, "SRR21966422", "SRX17949920", "SRS15467395", "SRP403311", "PRJNA891853", "Dendrimer targeted immunosuppression of microglia reactivity further enhances promotes photoreceptor regeneration kinetics in the zebrafish retina", "GSE216060", "Transcriptome Analysis", "We used a zebrafish model of inducible rod photoreceptor death and investsgate the effect of Dexamethasone and nanoparticle conjugated Dex on regeneration kinetics Overall design: We used bulk RNA seq to analyze expression of zebrafish eyes at 7 dpf that were untreated  treated with Mtz to kill rods  treated with Mtz + D Dex induce immunosupression or treated with D Dex alone", null, "pubmed:37202450", null, "NoMtzDDex Replicate 3", "GSM6658015", null, "source name:eye|tissue:eye|genotype:Tgrho:YFP Eco. NfsBgmc500|treatment:No Mtz to ablate rods but then injection with D Dex and 24h till recovery|age:7dpf", "NoMtzDDex Replicate 3", "Rstudio Raw sequencing data in the form of fasta.gz files was downloaded and unzipped and then terminal function cutadapt was used to remove Nextera sequencing adapters Samples were then read into fastqc for quality control to ensure proper and similarly sized libraries  complete removal of adapters and high sequence quality scores throughout. Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. NfsBgmc500|treatment:No Mtz to ablate rods but then injection with D Dex and 24h till recovery|age:7dpf", "GSM6658015", "GSM6658015: NoMtzDDex Replicate 3; Danio rerio; RNA Seq", "GSM6658015 r1", "GSM6658015", "1", "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4  Takara 634440 kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP403311", null, "loader:fastq load.py", "KEmm-No-Mtz-D-Dex-3_S12_L001_R1_001.fastq.gz", "fastq", 3963989800.0, 39639898.0, "GSM6658015 r1", "0:100", "A:1065080529;C:919828042;G:903598076;T:1075359802;N:123351", 100, null, null, null, 1065080529, 919828042, 903598076, 1075359802, 123351, "SRX17949920", "SRS15467395", "SRA1524004", "Mumm lab, Human Genetics, Johns Hopkins University", "Mumm lab, Human Genetics, Johns Hopkins University", 1, 0.92947, null, 0.16539, null, 0.69136, null, 0.42499, null, 100, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "United States", "2022-10-18", "Larval", "Larval", "Eye", "Sensory System"], [71734, "SRR21966423", "SRX17949920", "SRS15467395", "SRP403311", "PRJNA891853", "Dendrimer targeted immunosuppression of microglia reactivity further enhances promotes photoreceptor regeneration kinetics in the zebrafish retina", "GSE216060", "Transcriptome Analysis", "We used a zebrafish model of inducible rod photoreceptor death and investsgate the effect of Dexamethasone and nanoparticle conjugated Dex on regeneration kinetics Overall design: We used bulk RNA seq to analyze expression of zebrafish eyes at 7 dpf that were untreated  treated with Mtz to kill rods  treated with Mtz + D Dex induce immunosupression or treated with D Dex alone", null, "pubmed:37202450", null, "NoMtzDDex Replicate 3", "GSM6658015", null, "source name:eye|tissue:eye|genotype:Tgrho:YFP Eco. NfsBgmc500|treatment:No Mtz to ablate rods but then injection with D Dex and 24h till recovery|age:7dpf", "NoMtzDDex Replicate 3", "Rstudio Raw sequencing data in the form of fasta.gz files was downloaded and unzipped and then terminal function cutadapt was used to remove Nextera sequencing adapters Samples were then read into fastqc for quality control to ensure proper and similarly sized libraries  complete removal of adapters and high sequence quality scores throughout. Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. NfsBgmc500|treatment:No Mtz to ablate rods but then injection with D Dex and 24h till recovery|age:7dpf", "GSM6658015", "GSM6658015: NoMtzDDex Replicate 3; Danio rerio; RNA Seq", "GSM6658015 r1", "GSM6658015", "1", "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4  Takara 634440 kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP403311", null, "loader:fastq load.py", "KEmm-No-Mtz-D-Dex-3_S12_L002_R1_001.fastq.gz", "fastq", 3998326900.0, 39983269.0, "GSM6658015 r2", "0:100", "A:1074857657;C:927954385;G:910400506;T:1085020535;N:93817", 100, null, null, null, 1074857657, 927954385, 910400506, 1085020535, 93817, "SRX17949920", "SRS15467395", "SRA1524004", "Mumm lab, Human Genetics, Johns Hopkins University", "Mumm lab, Human Genetics, Johns Hopkins University", 1, 0.9279, null, 0.16573, null, 0.69294, null, 0.43018, null, 100, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "United States", "2022-10-18", "Larval", "Larval", "Eye", "Sensory System"], [71735, "SRR21966424", "SRX17949919", "SRS15467394", "SRP403311", "PRJNA891853", "Dendrimer targeted immunosuppression of microglia reactivity further enhances promotes photoreceptor regeneration kinetics in the zebrafish retina", "GSE216060", "Transcriptome Analysis", "We used a zebrafish model of inducible rod photoreceptor death and investsgate the effect of Dexamethasone and nanoparticle conjugated Dex on regeneration kinetics Overall design: We used bulk RNA seq to analyze expression of zebrafish eyes at 7 dpf that were untreated  treated with Mtz to kill rods  treated with Mtz + D Dex induce immunosupression or treated with D Dex alone", null, "pubmed:37202450", null, "NoMtzDDex Replicate 2", "GSM6658014", null, "source name:eye|tissue:eye|genotype:Tgrho:YFP Eco. NfsBgmc500|treatment:No Mtz to ablate rods but then injection with D Dex and 24h till recovery|age:7dpf", "NoMtzDDex Replicate 2", "Rstudio Raw sequencing data in the form of fasta.gz files was downloaded and unzipped and then terminal function cutadapt was used to remove Nextera sequencing adapters Samples were then read into fastqc for quality control to ensure proper and similarly sized libraries  complete removal of adapters and high sequence quality scores throughout. Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. NfsBgmc500|treatment:No Mtz to ablate rods but then injection with D Dex and 24h till recovery|age:7dpf", "GSM6658014", "GSM6658014: NoMtzDDex Replicate 2; Danio rerio; RNA Seq", "GSM6658014 r1", "GSM6658014", "1", "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4  Takara 634440 kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP403311", null, "loader:fastq load.py", "KEmm-No-Mtz-D-Dex-2_S11_L001_R1_001.fastq.gz", "fastq", 2928377400.0, 29283774.0, "GSM6658014 r1", "0:100", "A:782180809;C:685462701;G:671818266;T:788824815;N:90809", 100, null, null, null, 782180809, 685462701, 671818266, 788824815, 90809, "SRX17949919", "SRS15467394", "SRA1524004", "Mumm lab, Human Genetics, Johns Hopkins University", "Mumm lab, Human Genetics, Johns Hopkins University", 1, 0.93083, null, 0.13469, null, 0.70173, null, 0.42103, null, 100, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "United States", "2022-10-18", "Larval", "Larval", "Eye", "Sensory System"], [71736, "SRR21966425", "SRX17949919", "SRS15467394", "SRP403311", "PRJNA891853", "Dendrimer targeted immunosuppression of microglia reactivity further enhances promotes photoreceptor regeneration kinetics in the zebrafish retina", "GSE216060", "Transcriptome Analysis", "We used a zebrafish model of inducible rod photoreceptor death and investsgate the effect of Dexamethasone and nanoparticle conjugated Dex on regeneration kinetics Overall design: We used bulk RNA seq to analyze expression of zebrafish eyes at 7 dpf that were untreated  treated with Mtz to kill rods  treated with Mtz + D Dex induce immunosupression or treated with D Dex alone", null, "pubmed:37202450", null, "NoMtzDDex Replicate 2", "GSM6658014", null, "source name:eye|tissue:eye|genotype:Tgrho:YFP Eco. NfsBgmc500|treatment:No Mtz to ablate rods but then injection with D Dex and 24h till recovery|age:7dpf", "NoMtzDDex Replicate 2", "Rstudio Raw sequencing data in the form of fasta.gz files was downloaded and unzipped and then terminal function cutadapt was used to remove Nextera sequencing adapters Samples were then read into fastqc for quality control to ensure proper and similarly sized libraries  complete removal of adapters and high sequence quality scores throughout. Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. 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NfsBgmc500|treatment:No Mtz to ablate rods but then injection with D Dex and 24h till recovery|age:7dpf", "NoMtzDDex Replicate 1", "Rstudio Raw sequencing data in the form of fasta.gz files was downloaded and unzipped and then terminal function cutadapt was used to remove Nextera sequencing adapters Samples were then read into fastqc for quality control to ensure proper and similarly sized libraries  complete removal of adapters and high sequence quality scores throughout. Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. 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Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. 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Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. 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Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. 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Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. 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Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. 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Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. 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Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. 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Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. 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NfsBgmc500|treatment:24h Mtz to ablate rods  then injection with dendrimer conugated Dexamethas1 and 24h recovery before collection|age:7dpf", "MtzDDex Replicate 3", "Rstudio Raw sequencing data in the form of fasta.gz files was downloaded and unzipped and then terminal function cutadapt was used to remove Nextera sequencing adapters Samples were then read into fastqc for quality control to ensure proper and similarly sized libraries  complete removal of adapters and high sequence quality scores throughout. Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. 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NfsBgmc500|treatment:24h Mtz to ablate rods  then injection with dendrimer conugated Dexamethas1 and 24h recovery before collection|age:7dpf", "MtzDDex Replicate 2", "Rstudio Raw sequencing data in the form of fasta.gz files was downloaded and unzipped and then terminal function cutadapt was used to remove Nextera sequencing adapters Samples were then read into fastqc for quality control to ensure proper and similarly sized libraries  complete removal of adapters and high sequence quality scores throughout. Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. 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NfsBgmc500|treatment:24h Mtz to ablate rods  then injection with dendrimer conugated Dexamethas1 and 24h recovery before collection|age:7dpf", "MtzDDex Replicate 2", "Rstudio Raw sequencing data in the form of fasta.gz files was downloaded and unzipped and then terminal function cutadapt was used to remove Nextera sequencing adapters Samples were then read into fastqc for quality control to ensure proper and similarly sized libraries  complete removal of adapters and high sequence quality scores throughout. Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. 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NfsBgmc500|treatment:24h Mtz to ablate rods  then injection with dendrimer conugated Dexamethas1 and 24h recovery before collection|age:7dpf", "MtzDDex Replicate1", "Rstudio Raw sequencing data in the form of fasta.gz files was downloaded and unzipped and then terminal function cutadapt was used to remove Nextera sequencing adapters Samples were then read into fastqc for quality control to ensure proper and similarly sized libraries  complete removal of adapters and high sequence quality scores throughout. Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. 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Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. 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Sequencing for each sample occurred over two lanes and thus read files were combined using the \u201ccat\u201d terminal function Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto To identify differential expressed genes DEGs between conditions  a matrix file containing all Ensembl transcript ID\u2019s and 12 columns  one for each sample  were read into the edgeR Bioconductor package version 3.34.1 in R/R Studio versions 4.0.3 and 1.4.1103  respectively Assembly: GRCz11/danRer11 Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample", "eye", null, "RNA was extracted using the RNeasy Micro Kit Qiagen  74004 Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA v4 \u00a0Takara 634440 kit", null, "tissue:eye|genotype:Tgrho:YFP Eco. 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