metadata: run_metadata: 67 rows where experiment.library_layout = "SINGLE", technology = "bulk" and tissue

67 rows where experiment.library_layout = "SINGLE", technology = "bulk" and tissue_curation = "Eye"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
34913	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 / zebra…	pubmed:40114969	crim1 knockdown whole eyes 72 hpf sample 3	GSM8794307	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 ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 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 ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 in all datasets were identified by comparing crim1 / mutants with control datasets using an in house Python script.	Whole eye	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® 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′ end of the double stranded DNA post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ 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.	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® 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′ end of the double stranded DNA post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ 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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP563805		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	873905674	752237090	742087342	963442356	221444	SRX27670022	SRS24074877			Cincinnati Children's Hospital Medical Center							B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-02-13	Larval	Larval	Eye	Sensory System
34914	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 / zebra…	pubmed:40114969	crim1 knockdown whole eyes 72 hpf sample 2	GSM8794306	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 ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 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 ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 in all datasets were identified by comparing crim1 / mutants with control datasets using an in house Python script.	Whole eye	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® 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′ end of the double stranded DNA post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ 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.	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® 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′ end of the double stranded DNA post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ 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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP563805		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	907771486	794245897	783248243	1005559302	234116	SRX27670021	SRS24074876			Cincinnati Children's Hospital Medical Center							B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-02-13	Larval	Larval	Eye	Sensory System
34915	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 / zebra…	pubmed:40114969	crim1 knockdown whole eyes 72 hpf sample 1	GSM8794305	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 ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 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 ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 in all datasets were identified by comparing crim1 / mutants with control datasets using an in house Python script.	Whole eye	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® 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′ end of the double stranded DNA post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ 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.	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® 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′ end of the double stranded DNA post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ 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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP563805		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	714065903	618520760	607652792	811160146	267779	SRX27670020	SRS24074875			Cincinnati Children's Hospital Medical Center							B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-02-13	Larval	Larval	Eye	Sensory System
34916	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 / zebra…	pubmed:40114969	wildtype whole eyes 72 hpf sample 3	GSM8794304	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 ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 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 ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 in all datasets were identified by comparing crim1 / mutants with control datasets using an in house Python script.	Whole eye	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® 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′ end of the double stranded DNA post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ 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.	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® 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′ end of the double stranded DNA post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ 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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP563805		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	759373846	644323432	637932338	840046555	189805	SRX27670019	SRS24074874			Cincinnati Children's Hospital Medical Center							B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-02-13	Larval	Larval	Eye	Sensory System
34917	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 / zebra…	pubmed:40114969	wildtype whole eyes 72 hpf sample 2	GSM8794303	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 ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 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 ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 in all datasets were identified by comparing crim1 / mutants with control datasets using an in house Python script.	Whole eye	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® 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′ end of the double stranded DNA post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ 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.	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® 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′ end of the double stranded DNA post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ 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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP563805		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	617266566	538355433	528639561	696293971	224651	SRX27670018	SRS24074873			Cincinnati Children's Hospital Medical Center							B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-02-13	Larval	Larval	Eye	Sensory System
34918	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 / zebra…	pubmed:40114969	wildtype whole eyes 72 hpf sample 1	GSM8794302	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 ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 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 ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 in all datasets were identified by comparing crim1 / mutants with control datasets using an in house Python script.	Whole eye	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® 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′ end of the double stranded DNA post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ 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.	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® 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′ end of the double stranded DNA post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ 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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP563805		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	783035033	680405728	668894784	875142229	280826	SRX27670017	SRS24074872			Cincinnati Children's Hospital Medical Center							B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-02-13	Larval	Larval	Eye	Sensory System
60457	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.	pubmed:33634099	36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 3	GSM4681961	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	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	treatment:Torrin\|age:36hpf\|tissue:eyes	GSM4681961	GSM4681961: 36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 3; Danio rerio; RNA Seq	GSM4681961		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	SRP273065		Tor_3.fq	fastq	611438450.0	12228769.0	GSM4681961 r1	0:50	A:155737074;C:142979561;G:143702101;T:169019714;N:0	50	155737074	142979561	143702101	169019714	0	SRX8790734	SRS7059126	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.96219	0.1228	0.73219	0.50697	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60458	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.	pubmed:33634099	36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 2	GSM4681960	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	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	treatment:Torrin\|age:36hpf\|tissue:eyes	GSM4681960	GSM4681960: 36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 2; Danio rerio; RNA Seq	GSM4681960		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	SRP273065		Tor_2.fq	fastq	610161700.0	12203234.0	GSM4681960 r1	0:50	A:153768852;C:143410611;G:145248964;T:167733273;N:0	50	153768852	143410611	145248964	167733273	0	SRX8790733	SRS7059125	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.96418	0.12127	0.73521	0.50591	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60459	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.	pubmed:33634099	36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 1	GSM4681959	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	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	treatment:Torrin\|age:36hpf\|tissue:eyes	GSM4681959	GSM4681959: 36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 1; Danio rerio; RNA Seq	GSM4681959		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	SRP273065		Tor_1.fq	fastq	568616650.0	11372333.0	GSM4681959 r1	0:50	A:143342391;C:133596830;G:136056983;T:155620446;N:0	50	143342391	133596830	136056983	155620446	0	SRX8790732	SRS7059124	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.96423	0.1166	0.73811	0.50869	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60460	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.	pubmed:33634099	36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 3	GSM4681958	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	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	treatment:DMSO control\|age:36hpf\|tissue:eyes	GSM4681958	GSM4681958: 36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 3; Danio rerio; RNA Seq	GSM4681958		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	SRP273065		DMSO_3.fq	fastq	710747750.0	14214955.0	GSM4681958 r1	0:50	A:184360596;C:160789051;G:160903077;T:204668511;N:26515	50	184360596	160789051	160903077	204668511	26515	SRX8790731	SRS7059123	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.92693	0.14102	0.74233	0.52477	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60461	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.	pubmed:33634099	36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 2	GSM4681957	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	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	treatment:DMSO control\|age:36hpf\|tissue:eyes	GSM4681957	GSM4681957: 36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 2; Danio rerio; RNA Seq	GSM4681957		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	SRP273065		DMSO_2.fq	fastq	710470350.0	14209407.0	GSM4681957 r1	0:50	A:180578463;C:165554366;G:164357951;T:199952943;N:26627	50	180578463	165554366	164357951	199952943	26627	SRX8790730	SRS7059122	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.92993	0.12326	0.73316	0.50795	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60462	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.	pubmed:33634099	36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 1	GSM4681956	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	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	treatment:DMSO control\|age:36hpf\|tissue:eyes	GSM4681956	GSM4681956: 36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 1; Danio rerio; RNA Seq	GSM4681956		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	SRP273065		DMSO_1.fq	fastq	684145550.0	13682911.0	GSM4681956 r1	0:50	A:176031808;C:157711101;G:157012646;T:193364628;N:25367	50	176031808	157711101	157012646	193364628	25367	SRX8790729	SRS7059121	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.93134	0.11826	0.73742	0.51639	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60463	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.	pubmed:33634099	36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 3	GSM4681955	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	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	genotype:Wnt2ba overexpression\|age:36hpf\|tissue:eyes	GSM4681955	GSM4681955: 36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 3; Danio rerio; RNA Seq	GSM4681955		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	SRP273065		Wnt2b_3.fq	fastq	1683174573.0	33003423.0	GSM4681955 r1	0:51	A:425533518;C:379417030;G:382377050;T:466758495;N:29088480	51	425533518	379417030	382377050	466758495	29088480	SRX8790728	SRS7059120	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.92087	0.07926	0.72699	0.50196	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60464	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.	pubmed:33634099	36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 2	GSM4681954	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	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	genotype:Wnt2ba overexpression\|age:36hpf\|tissue:eyes	GSM4681954	GSM4681954: 36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 2; Danio rerio; RNA Seq	GSM4681954		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	SRP273065		Wnt2b_2.fq	fastq	1491166815.0	29238565.0	GSM4681954 r1	0:51	A:378958250;C:335771876;G:337239729;T:413432220;N:25764740	51	378958250	335771876	337239729	413432220	25764740	SRX8790727	SRS7059119	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.92209	0.08083	0.733	0.51077	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60465	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.	pubmed:33634099	36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 1	GSM4681953	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	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	genotype:Wnt2ba overexpression\|age:36hpf\|tissue:eyes	GSM4681953	GSM4681953: 36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 1; Danio rerio; RNA Seq	GSM4681953		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	SRP273065		Wnt2b_1.fq	fastq	1919112507.0	37629657.0	GSM4681953 r1	0:51	A:477418936;C:433410513;G:453965639;T:530637937;N:23679482	51	477418936	433410513	453965639	530637937	23679482	SRX8790726	SRS7059118	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.78015	0.06857	0.73608	0.49023	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60466	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.	pubmed:33634099	YapS87A replicate3	GSM4681952	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	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	genotype:YapS87A overexpression\|age:36hpf\|tissue:eyes	GSM4681952	GSM4681952: YapS87A replicate3; Danio rerio; RNA Seq	GSM4681952		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	SRP273065		YapS87A_3_sequence.txt	fastq	1680502581.0	32951031.0	GSM4681952 r1	0:51	A:431882743;C:376993099;G:378520286;T:464147117;N:28959336	51	431882743	376993099	378520286	464147117	28959336	SRX8790725	SRS7059117	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.9063	0.08494	0.73308	0.45344	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60467	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.	pubmed:33634099	YapS87A replicate2	GSM4681951	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	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	genotype:YapS87A overexpression\|age:36hpf\|tissue:eyes	GSM4681951	GSM4681951: YapS87A replicate2; Danio rerio; RNA Seq	GSM4681951		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	SRP273065		YapS87A_2_sequence.txt	fastq	1742004705.0	34156955.0	GSM4681951 r1	0:51	A:447373634;C:393295480;G:396777263;T:483090843;N:21467485	51	447373634	393295480	396777263	483090843	21467485	SRX8790724	SRS7059116	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.90564	0.08572	0.72721	0.46483	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60468	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.	pubmed:33634099	YapS87A replicate1	GSM4681950	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	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	genotype:YapS87A overexpression\|age:36hpf\|tissue:eyes	GSM4681950	GSM4681950: YapS87A replicate1; Danio rerio; RNA Seq	GSM4681950		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	SRP273065		YapS87A_1_sequence.txt	fastq	1605602451.0	31482401.0	GSM4681950 r1	0:51	A:416296166;C:357147049;G:359581538;T:444847570;N:27730128	51	416296166	357147049	359581538	444847570	27730128	SRX8790723	SRS7059115	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.90205	0.08929	0.72949	0.47221	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60469	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.	pubmed:33634099	36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate3	GSM4681949	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	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	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		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	SRP273065		WT_3_sequence.txt	fastq	1609588305.0	31560555.0	GSM4681949 r1	0:51	A:412663150;C:358619332;G:364439350;T:446055681;N:27810792	51	412663150	358619332	364439350	446055681	27810792	SRX8790722	SRS7059114	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.92187	0.07809	0.73517	0.46998	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60470	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.	pubmed:33634099	36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate2	GSM4681948	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	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	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		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	SRP273065		WT_2_sequence.txt	fastq	1637145594.0	32100894.0	GSM4681948 r1	0:51	A:414176151;C:369403072;G:372539483;T:452762354;N:28264534	51	414176151	369403072	372539483	452762354	28264534	SRX8790721	SRS7059113	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.92354	0.08166	0.73174	0.47515	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60471	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.	pubmed:33634099	36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate1	GSM4681947	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	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	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		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	SRP273065		WT_1_sequence.txt	fastq	1666445961.0	32675411.0	GSM4681947 r1	0:51	A:421437796;C:380026405;G:379400332;T:465027467;N:20553961	51	421437796	380026405	379400332	465027467	20553961	SRX8790720	SRS7059112	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.91939	0.07636	0.73052	0.4731	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60472	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.	pubmed:33634099	36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 3	GSM4681946	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	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	genotype:NICD overexpression\|age:36hpf\|tissue:eyes	GSM4681946	GSM4681946: 36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 3; Danio rerio; RNA Seq	GSM4681946		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	SRP273065		NICD_3.fq	fastq	1687493202.0	33088102.0	GSM4681946 r1	0:51	A:466000780;C:363861781;G:362676818;T:465728464;N:29225359	51	466000780	363861781	362676818	465728464	29225359	SRX8790719	SRS7059111	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.90234	0.10242	0.71488	0.47661	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60473	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.	pubmed:33634099	36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 2	GSM4681945	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	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	genotype:NICD overexpression\|age:36hpf\|tissue:eyes	GSM4681945	GSM4681945: 36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 2; Danio rerio; RNA Seq	GSM4681945		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	SRP273065		NICD_2.fq	fastq	1724098248.0	33805848.0	GSM4681945 r1	0:51	A:479329096;C:373215849;G:370751023;T:475738259;N:25064021	51	479329096	373215849	370751023	475738259	25064021	SRX8790718	SRS7059110	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.90041	0.1068	0.71571	0.48007	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60474	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.	pubmed:33634099	36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 1	GSM4681944	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	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	genotype:NICD overexpression\|age:36hpf\|tissue:eyes	GSM4681944	GSM4681944: 36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 1; Danio rerio; RNA Seq	GSM4681944		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	SRP273065		NICD_1.fq	fastq	1929410682.0	37831582.0	GSM4681944 r1	0:51	A:531140272;C:421394845;G:418288095;T:530541126;N:28046344	51	531140272	421394845	418288095	530541126	28046344	SRX8790717	SRS7059109	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.90898	0.10574	0.71898	0.47601	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60475	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.	pubmed:33634099	36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 6	GSM4681943	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	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	genotype:NICD Control\|age:36hpf\|tissue:eyes	GSM4681943	GSM4681943: 36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 6; Danio rerio; RNA Seq	GSM4681943		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	SRP273065		NICD_Control_6.fq	fastq	2023785927.0	39682077.0	GSM4681943 r1	0:51	A:561742336;C:444105929;G:439290439;T:558958186;N:19689037	51	561742336	444105929	439290439	558958186	19689037	SRX8790716	SRS7059108	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.91779	0.10376	0.72468	0.46199	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60476	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.	pubmed:33634099	36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 5	GSM4681942	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	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	genotype:NICD Control\|age:36hpf\|tissue:eyes	GSM4681942	GSM4681942: 36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 5; Danio rerio; RNA Seq	GSM4681942		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	SRP273065		NICD_Control_5.fq	fastq	1740124386.0	34120086.0	GSM4681942 r1	0:51	A:465085934;C:391698178;G:386868685;T:479536883;N:16934706	51	465085934	391698178	386868685	479536883	16934706	SRX8790715	SRS7059107	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.92122	0.09508	0.72606	0.47404	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60477	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.	pubmed:33634099	36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 1	GSM4681941	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	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	genotype:NICD Control\|age:36hpf\|tissue:eyes	GSM4681941	GSM4681941: 36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 1; Danio rerio; RNA Seq	GSM4681941		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	SRP273065		NICD_Control_1.fq	fastq	1876256595.0	36789345.0	GSM4681941 r1	0:51	A:505568821;C:417420484;G:410313801;T:515696712;N:27256777	51	505568821	417420484	410313801	515696712	27256777	SRX8790714	SRS7059106	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.91459	0.09419	0.72512	0.46824	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60478	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.	pubmed:33634099	36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 3	GSM4681940	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	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	genotype:Rab11aDN overexpression\|age:36hpf\|tissue:eyes	GSM4681940	GSM4681940: 36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 3; Danio rerio; RNA Seq	GSM4681940		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	SRP273065		Rab11aDN_3.fq	fastq	1937833026.0	37996726.0	GSM4681940 r1	0:51	A:519376884;C:429809002;G:419678420;T:530881829;N:38086891	51	519376884	429809002	419678420	530881829	38086891	SRX8790713	SRS7059105	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.9087	0.1008	0.72705	0.47617	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60479	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.	pubmed:33634099	36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 2	GSM4681939	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	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	genotype:Rab11aDN overexpression\|age:36hpf\|tissue:eyes	GSM4681939	GSM4681939: 36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 2; Danio rerio; RNA Seq	GSM4681939		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	SRP273065		Rab11aDN_2.fq	fastq	1538149392.0	30159792.0	GSM4681939 r1	0:51	A:404899388;C:344011831;G:336575868;T:422430316;N:30231989	51	404899388	344011831	336575868	422430316	30231989	SRX8790712	SRS7059104	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.91044	0.09831	0.72801	0.47546	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60480	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.	pubmed:33634099	36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 1	GSM4681938	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	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	genotype:Rab11aDN overexpression\|age:36hpf\|tissue:eyes	GSM4681938	GSM4681938: 36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 1; Danio rerio; RNA Seq	GSM4681938		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	SRP273065		Rab11aDN_1.fq	fastq	1642073673.0	32197523.0	GSM4681938 r1	0:51	A:429811686;C:368457771;G:362183885;T:449347598;N:32272733	51	429811686	368457771	362183885	449347598	32272733	SRX8790711	SRS7059103	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.90921	0.09675	0.73133	0.4816	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60481	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.	pubmed:33634099	36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 3	GSM4681937	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	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	genotype:Rab11aDN Control\|age:36hpf\|tissue:eyes	GSM4681937	GSM4681937: 36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 3; Danio rerio; RNA Seq	GSM4681937		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	SRP273065		Rab11aDN_Control_3.fq	fastq	1580663604.0	30993404.0	GSM4681937 r1	0:51	A:412500071;C:356327817;G:348043781;T:432725076;N:31066859	51	412500071	356327817	348043781	432725076	31066859	SRX8790710	SRS7059102	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.91358	0.09416	0.72756	0.47659	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60482	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.	pubmed:33634099	36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 2	GSM4681936	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	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	genotype:Rab11aDN Control\|age:36hpf\|tissue:eyes	GSM4681936	GSM4681936: 36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 2; Danio rerio; RNA Seq	GSM4681936		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	SRP273065		Rab11aDN_Control_2.fq	fastq	1508085198.0	29570298.0	GSM4681936 r1	0:51	A:389591011;C:341465324;G:334342859;T:413045227;N:29640777	51	389591011	341465324	334342859	413045227	29640777	SRX8790709	SRS7059101	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.91681	0.09096	0.72908	0.47951	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
60483	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.	pubmed:33634099	36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 1	GSM4681935	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	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	genotype:Rab11aDN Control\|age:36hpf\|tissue:eyes	GSM4681935	GSM4681935: 36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 1; Danio rerio; RNA Seq	GSM4681935		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	SRP273065		Rab11aDN_Control_1.fq	fastq	2010222018.0	39416118.0	GSM4681935 r1	0:51	A:517848834;C:456636261;G:445209526;T:551017897;N:39509500	51	517848834	456636261	445209526	551017897	39509500	SRX8790708	SRS7059100	SRA1102335	GEO	Clark, Ophthalmology and Visual Sciences, Washington University	1	0.91683	0.09045	0.73105	0.4712	51	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2020-07-22	Pharyngula	Embryo	Eye	Sensory System
67683	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.			BBS1 MUT 10dpf S1	strain:Bbs1ka742\|age:10dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype: / \|Paired group:D\|BioSampleModel:Model organism or animal							RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 MUT 10dpf S1	BBS1 MUT 10dpf S1	TruSeq Stranded Total RNA Library Prep Gold			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	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	951181543	805662797	846180468	1032919946	41091	SRX13414611	SRS11316492	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.93818	0.32197	0.69451	0.47394	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67684	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.			BBS1 CTRL 10dpf S3	strain:Bbs1ka742\|age:10dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype:+/ \|Paired group:F\|BioSampleModel:Model organism or animal							RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 CTRL 10dpf S3	BBS1 CTRL 10dpf S3	TruSeq Stranded Total RNA Library Prep Gold			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	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	814143728	694726254	728135378	893834285	35653	SRX13414610	SRS11316490	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.94014	0.33329	0.69735	0.47408	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67685	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.			BBS1 CTRL 10dpf S2	strain:Bbs1ka742\|age:10dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype:+/ \|Paired group:E\|BioSampleModel:Model organism or animal							RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 CTRL 10dpf S2	BBS1 CTRL 10dpf S2	TruSeq Stranded Total RNA Library Prep Gold			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	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	786649223	679725108	723425238	872929361	34816	SRX13414609	SRS11316491	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.94626	0.26532	0.68793	0.46861	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67686	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.			BBS1 Ctrl 10dpf S1	strain:Bbs1ka742\|age:10dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype:+/ \|Paired group:D\|BioSampleModel:Model organism or animal							RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 Ctrl 10dpf S1	BBS1 Ctrl 10dpf S1	TruSeq Stranded Total RNA Library Prep Gold			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	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	1141948730	979155774	1019331809	1247901031	49213	SRX13414608	SRS11316489	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.94326	0.28573	0.69296	0.47244	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67687	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.			BBS1 MUT 5dpf S3	strain:Bbs1ka742\|age:5dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype: / \|Paired group:C\|BioSampleModel:Model organism or animal							RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 MUT 5dpf S3	BBS1 MUT 5dpf S3	TruSeq Stranded Total RNA Library Prep Gold			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	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	813926164	646079228	694857531	875585698	33753	SRX13414607	SRS11316488	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.92861	0.41464	0.69051	0.49332	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67688	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.			BBS1 MUT 5dpf S2	strain:Bbs1ka742\|age:5dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype: / \|Paired group:B\|BioSampleModel:Model organism or animal							RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 MUT 5dpf S2	BBS1 MUT 5dpf S2	TruSeq Stranded Total RNA Library Prep Gold			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	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	968857332	821571707	867307403	1056625911	41816	SRX13414606	SRS11316487	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.93912	0.32694	0.68781	0.48549	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67689	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.			BBS1 MUT 5dpf S1	strain:Bbs1ka742\|age:5dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype: / \|Paired group:A\|BioSampleModel:Model organism or animal							RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 MUT 5dpf S1	BBS1 MUT 5dpf S1	TruSeq Stranded Total RNA Library Prep Gold			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	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	977907912	830475992	855441672	1036029492	41381	SRX13414605	SRS11316486	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.93133	0.40806	0.69562	0.5114	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67690	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.			BBS1 CTRL 5dpf S3	strain:Bbs1ka742\|age:5dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype:+/ \|Paired group:C\|BioSampleModel:Model organism or animal							RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 CTRL 5dpf S3	BBS1 CTRL 5dpf S3	TruSeq Stranded Total RNA Library Prep Gold			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	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	910433958	775887812	822289434	996540997	40058	SRX13414604	SRS11316485	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.94274	0.28843	0.68678	0.47383	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67691	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.			BBS1 MUT 10dpf S3	strain:Bbs1ka742\|age:10dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype: / \|Paired group:F\|BioSampleModel:Model organism or animal							RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 MUT 10dpf S3	BBS1 MUT 10dpf S3	TruSeq Stranded Total RNA Library Prep Gold			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	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	1019329287	820362185	870436357	1111106893	43031	SRX13414603	SRS11316483	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.93021	0.40772	0.70019	0.47824	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67692	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.			BBS1 MUT 10dpf S2	strain:Bbs1ka742\|age:10dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype: / \|Paired group:E\|BioSampleModel:Model organism or animal							RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 MUT 10dpf S2	BBS1 MUT 10dpf S2	TruSeq Stranded Total RNA Library Prep Gold			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	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	726140802	605265574	628347573	788063451	30863	SRX13414602	SRS11316484	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.93216	0.39301	0.70009	0.50624	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67693	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.			BBS1 CTRL 5dpf S2	strain:Bbs1ka742\|age:5dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype:+/ \|Paired group:B\|BioSampleModel:Model organism or animal							RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 CTRL 5dpf S2	BBS1 CTRL 5dpf S2	TruSeq Stranded Total RNA Library Prep Gold			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	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	865249225	752466820	799272800	954431124	37533	SRX13414601	SRS11316482	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.94297	0.30382	0.68523	0.49502	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67694	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.			BBS1 CTRL 5dpf S1	strain:Bbs1ka742\|age:5dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype:+/ \|Paired group:A\|BioSampleModel:Model organism or animal							RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 CTRL 5dpf S1	BBS1 CTRL 5dpf S1	TruSeq Stranded Total RNA Library Prep Gold			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	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	886651528	694664952	729637645	932951711	36588	SRX13414600	SRS11316481	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.92662	0.42838	0.69404	0.48808	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
71733	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	pubmed:37202450	NoMtzDDex Replicate 3	GSM6658015	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 “cat” 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’s 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	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	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	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	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	0.16539	0.69136	0.42499	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71734	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	pubmed:37202450	NoMtzDDex Replicate 3	GSM6658015	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 “cat” 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’s 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	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	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	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	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	0.16573	0.69294	0.43018	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71735	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	pubmed:37202450	NoMtzDDex Replicate 2	GSM6658014	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 “cat” 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’s 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	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	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	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	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	0.13469	0.70173	0.42103	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71736	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	pubmed:37202450	NoMtzDDex Replicate 2	GSM6658014	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 “cat” 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’s 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	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	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	loader:fastq load.py	KEmm-No-Mtz-D-Dex-2_S11_L002_R1_001.fastq.gz	fastq	3086327800.0	30863278.0	GSM6658014 r2	0:100	A:824138386;C:723454752;G:708299763;T:830361801;N:73098	100	824138386	723454752	708299763	830361801	73098	SRX17949919	SRS15467394	SRA1524004	Mumm lab, Human Genetics, Johns Hopkins University	Mumm lab, Human Genetics, Johns Hopkins University	1	0.92973	0.13395	0.70242	0.42614	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71737	71737	SRR21966426	SRX17949918	SRS15467393	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	pubmed:37202450	NoMtzDDex Replicate 1	GSM6658013	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 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 “cat” 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’s 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	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	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	GSM6658013	GSM6658013: NoMtzDDex Replicate 1; Danio rerio; RNA Seq	GSM6658013 r1	GSM6658013	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	loader:fastq load.py	KEmm-No-Mtz-D-Dex-1_S10_L001_R1_001.fastq.gz	fastq	3291249700.0	32912497.0	GSM6658013 r1	0:100	A:880967641;C:762730807;G:756683992;T:890762938;N:104322	100	880967641	762730807	756683992	890762938	104322	SRX17949918	SRS15467393	SRA1524004	Mumm lab, Human Genetics, Johns Hopkins University	Mumm lab, Human Genetics, Johns Hopkins University	1	0.93183	0.14423	0.69895	0.43005	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71738	71738	SRR21966427	SRX17949918	SRS15467393	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	pubmed:37202450	NoMtzDDex Replicate 1	GSM6658013	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 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 “cat” 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’s 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	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	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	GSM6658013	GSM6658013: NoMtzDDex Replicate 1; Danio rerio; RNA Seq	GSM6658013 r1	GSM6658013	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	loader:fastq load.py	KEmm-No-Mtz-D-Dex-1_S10_L002_R1_001.fastq.gz	fastq	3338299400.0	33382994.0	GSM6658013 r2	0:100	A:894013653;C:774035182;G:767143542;T:903026015;N:81008	100	894013653	774035182	767143542	903026015	81008	SRX17949918	SRS15467393	SRA1524004	Mumm lab, Human Genetics, Johns Hopkins University	Mumm lab, Human Genetics, Johns Hopkins University	1	0.9307	0.14395	0.69783	0.42727	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71739	71739	SRR21966428	SRX17949917	SRS15467392	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	pubmed:37202450	NoMtz Replicate 3	GSM6658012	source name:eye\|tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:Untreated controls\|age:7dpf	NoMtz 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 “cat” 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’s 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	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	tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:Untreated controls\|age:7dpf	GSM6658012	GSM6658012: NoMtz Replicate 3; Danio rerio; RNA Seq	GSM6658012 r1	GSM6658012	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	loader:fastq load.py	KEmm-No-Mtz-3_S9_L001_R1_001.fastq.gz	fastq	2142722300.0	21427223.0	GSM6658012 r1	0:100	A:576455453;C:493674256;G:490912516;T:581609745;N:70330	100	576455453	493674256	490912516	581609745	70330	SRX17949917	SRS15467392	SRA1524004	Mumm lab, Human Genetics, Johns Hopkins University	Mumm lab, Human Genetics, Johns Hopkins University	1	0.9327	0.15196	0.70378	0.42425	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71740	71740	SRR21966429	SRX17949917	SRS15467392	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	pubmed:37202450	NoMtz Replicate 3	GSM6658012	source name:eye\|tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:Untreated controls\|age:7dpf	NoMtz 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 “cat” 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’s 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	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	tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:Untreated controls\|age:7dpf	GSM6658012	GSM6658012: NoMtz Replicate 3; Danio rerio; RNA Seq	GSM6658012 r1	GSM6658012	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	loader:fastq load.py	KEmm-No-Mtz-3_S9_L002_R1_001.fastq.gz	fastq	2247481100.0	22474811.0	GSM6658012 r2	0:100	A:604765214;C:517907350;G:514978924;T:609771868;N:57744	100	604765214	517907350	514978924	609771868	57744	SRX17949917	SRS15467392	SRA1524004	Mumm lab, Human Genetics, Johns Hopkins University	Mumm lab, Human Genetics, Johns Hopkins University	1	0.9324	0.15199	0.7052	0.42503	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71741	71741	SRR21966430	SRX17949916	SRS15467391	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	pubmed:37202450	NoMtz Replicate 2	GSM6658011	source name:eye\|tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:Untreated controls\|age:7dpf	NoMtz 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 “cat” 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’s 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	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	tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:Untreated controls\|age:7dpf	GSM6658011	GSM6658011: NoMtz Replicate 2; Danio rerio; RNA Seq	GSM6658011 r1	GSM6658011	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	loader:fastq load.py	KEmm-No-Mtz-2_S8_L001_R1_001.fastq.gz	fastq	3430698500.0	34306985.0	GSM6658011 r1	0:100	A:918652910;C:812504339;G:766881039;T:932569452;N:90760	100	918652910	812504339	766881039	932569452	90760	SRX17949916	SRS15467391	SRA1524004	Mumm lab, Human Genetics, Johns Hopkins University	Mumm lab, Human Genetics, Johns Hopkins University	1	0.91343	0.16075	0.70885	0.4156	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71742	71742	SRR21966431	SRX17949916	SRS15467391	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	pubmed:37202450	NoMtz Replicate 2	GSM6658011	source name:eye\|tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:Untreated controls\|age:7dpf	NoMtz 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 “cat” 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’s 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	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	tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:Untreated controls\|age:7dpf	GSM6658011	GSM6658011: NoMtz Replicate 2; Danio rerio; RNA Seq	GSM6658011 r1	GSM6658011	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	loader:fastq load.py	KEmm-No-Mtz-2_S8_L002_R1_001.fastq.gz	fastq	3507479100.0	35074791.0	GSM6658011 r2	0:100	A:940154075;C:830847645;G:782282288;T:954125497;N:69595	100	940154075	830847645	782282288	954125497	69595	SRX17949916	SRS15467391	SRA1524004	Mumm lab, Human Genetics, Johns Hopkins University	Mumm lab, Human Genetics, Johns Hopkins University	1	0.91253	0.15998	0.70701	0.41689	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71743	71743	SRR21966432	SRX17949915	SRS15467390	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	pubmed:37202450	NoMtz Replicate 1	GSM6658010	source name:eye\|tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:Untreated controls\|age:7dpf	NoMtz 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 “cat” 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’s 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	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	tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:Untreated controls\|age:7dpf	GSM6658010	GSM6658010: NoMtz Replicate 1; Danio rerio; RNA Seq	GSM6658010 r1	GSM6658010	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	loader:fastq load.py	KEmm-No-Mtz-1_S7_L001_R1_001.fastq.gz	fastq	2643592300.0	26435923.0	GSM6658010 r1	0:100	A:705588786;C:626200626;G:595335765;T:716386850;N:80273	100	705588786	626200626	595335765	716386850	80273	SRX17949915	SRS15467390	SRA1524004	Mumm lab, Human Genetics, Johns Hopkins University	Mumm lab, Human Genetics, Johns Hopkins University	1	0.92891	0.14607	0.69986	0.41884	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71744	71744	SRR21966433	SRX17949915	SRS15467390	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	pubmed:37202450	NoMtz Replicate 1	GSM6658010	source name:eye\|tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:Untreated controls\|age:7dpf	NoMtz 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 “cat” 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’s 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	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	tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:Untreated controls\|age:7dpf	GSM6658010	GSM6658010: NoMtz Replicate 1; Danio rerio; RNA Seq	GSM6658010 r1	GSM6658010	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	loader:fastq load.py	KEmm-No-Mtz-1_S7_L002_R1_001.fastq.gz	fastq	2703583100.0	27035831.0	GSM6658010 r2	0:100	A:721838413;C:640835410;G:608179841;T:732666310;N:63126	100	721838413	640835410	608179841	732666310	63126	SRX17949915	SRS15467390	SRA1524004	Mumm lab, Human Genetics, Johns Hopkins University	Mumm lab, Human Genetics, Johns Hopkins University	1	0.92707	0.1457	0.70295	0.41742	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71745	71745	SRR21966434	SRX17949914	SRS15467389	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	pubmed:37202450	MtzDDex Replicate 3	GSM6658009	source name:eye\|tissue:eye\|genotype:Tgrho:YFP Eco. 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 “cat” 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’s 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	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	tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:24h Mtz to ablate rods then injection with dendrimer conugated Dexamethas1 and 24h recovery before collection\|age:7dpf	GSM6658009	GSM6658009: MtzDDex Replicate 3; Danio rerio; RNA Seq	GSM6658009 r1	GSM6658009	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	loader:fastq load.py	KEmm-Mtz-D-Dex-3_S6_L001_R1_001.fastq.gz	fastq	2738485000.0	27384850.0	GSM6658009 r1	0:100	A:734851504;C:638845736;G:616388105;T:748321233;N:78422	100	734851504	638845736	616388105	748321233	78422	SRX17949914	SRS15467389	SRA1524004	Mumm lab, Human Genetics, Johns Hopkins University	Mumm lab, Human Genetics, Johns Hopkins University	1	0.92788	0.14389	0.69934	0.43402	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71746	71746	SRR21966435	SRX17949914	SRS15467389	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	pubmed:37202450	MtzDDex Replicate 3	GSM6658009	source name:eye\|tissue:eye\|genotype:Tgrho:YFP Eco. 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 “cat” 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’s 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	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	tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:24h Mtz to ablate rods then injection with dendrimer conugated Dexamethas1 and 24h recovery before collection\|age:7dpf	GSM6658009	GSM6658009: MtzDDex Replicate 3; Danio rerio; RNA Seq	GSM6658009 r1	GSM6658009	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	loader:fastq load.py	KEmm-Mtz-D-Dex-3_S6_L002_R1_001.fastq.gz	fastq	2883222900.0	28832229.0	GSM6658009 r2	0:100	A:773580885;C:673456442;G:648869453;T:787254197;N:61923	100	773580885	673456442	648869453	787254197	61923	SRX17949914	SRS15467389	SRA1524004	Mumm lab, Human Genetics, Johns Hopkins University	Mumm lab, Human Genetics, Johns Hopkins University	1	0.92715	0.14452	0.6994	0.4374	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71747	71747	SRR21966436	SRX17949913	SRS15467388	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	pubmed:37202450	MtzDDex Replicate 2	GSM6658008	source name:eye\|tissue:eye\|genotype:Tgrho:YFP Eco. 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 “cat” 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’s 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	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	tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:24h Mtz to ablate rods then injection with dendrimer conugated Dexamethas1 and 24h recovery before collection\|age:7dpf	GSM6658008	GSM6658008: MtzDDex Replicate 2; Danio rerio; RNA Seq	GSM6658008 r1	GSM6658008	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	loader:fastq load.py	KEmm-Mtz-D-Dex-2_S5_L001_R1_001.fastq.gz	fastq	3044899300.0	30448993.0	GSM6658008 r1	0:100	A:820763750;C:722629334;G:675343694;T:826063979;N:98543	100	820763750	722629334	675343694	826063979	98543	SRX17949913	SRS15467388	SRA1524004	Mumm lab, Human Genetics, Johns Hopkins University	Mumm lab, Human Genetics, Johns Hopkins University	1	0.91674	0.13477	0.70319	0.43371	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71748	71748	SRR21966437	SRX17949913	SRS15467388	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	pubmed:37202450	MtzDDex Replicate 2	GSM6658008	source name:eye\|tissue:eye\|genotype:Tgrho:YFP Eco. 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 “cat” 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’s 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	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	tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:24h Mtz to ablate rods then injection with dendrimer conugated Dexamethas1 and 24h recovery before collection\|age:7dpf	GSM6658008	GSM6658008: MtzDDex Replicate 2; Danio rerio; RNA Seq	GSM6658008 r1	GSM6658008	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	loader:fastq load.py	KEmm-Mtz-D-Dex-2_S5_L002_R1_001.fastq.gz	fastq	3164456600.0	31644566.0	GSM6658008 r2	0:100	A:853253606;C:751756711;G:701124151;T:858242662;N:79470	100	853253606	751756711	701124151	858242662	79470	SRX17949913	SRS15467388	SRA1524004	Mumm lab, Human Genetics, Johns Hopkins University	Mumm lab, Human Genetics, Johns Hopkins University	1	0.91669	0.13432	0.70431	0.43173	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71749	71749	SRR21966438	SRX17949912	SRS15467387	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	pubmed:37202450	MtzDDex Replicate1	GSM6658007	source name:eye\|tissue:eye\|genotype:Tgrho:YFP Eco. 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 “cat” 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’s 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	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	tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:24h Mtz to ablate rods then injection with dendrimer conugated Dexamethas1 and 24h recovery before collection\|age:7dpf	GSM6658007	GSM6658007: MtzDDex Replicate1; Danio rerio; RNA Seq	GSM6658007 r1	GSM6658007	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	loader:fastq load.py	KEmm-Mtz-D-Dex-1_S4_L001_R1_001.fastq.gz	fastq	2795316000.0	27953160.0	GSM6658007 r1	0:100	A:743633662;C:665680059;G:627236908;T:758680271;N:85100	100	743633662	665680059	627236908	758680271	85100	SRX17949912	SRS15467387	SRA1524004	Mumm lab, Human Genetics, Johns Hopkins University	Mumm lab, Human Genetics, Johns Hopkins University	1	0.92616	0.13503	0.6984	0.43275	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71750	71750	SRR21966439	SRX17949912	SRS15467387	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	pubmed:37202450	MtzDDex Replicate1	GSM6658007	source name:eye\|tissue:eye\|genotype:Tgrho:YFP Eco. 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 “cat” 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’s 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	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	tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:24h Mtz to ablate rods then injection with dendrimer conugated Dexamethas1 and 24h recovery before collection\|age:7dpf	GSM6658007	GSM6658007: MtzDDex Replicate1; Danio rerio; RNA Seq	GSM6658007 r1	GSM6658007	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	loader:fastq load.py	KEmm-Mtz-D-Dex-1_S4_L002_R1_001.fastq.gz	fastq	2843398400.0	28433984.0	GSM6658007 r2	0:100	A:756744381;C:677526671;G:636933070;T:772129335;N:64943	100	756744381	677526671	636933070	772129335	64943	SRX17949912	SRS15467387	SRA1524004	Mumm lab, Human Genetics, Johns Hopkins University	Mumm lab, Human Genetics, Johns Hopkins University	1	0.925	0.13597	0.69808	0.43551	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71751	71751	SRR21966440	SRX17949911	SRS15467386	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	pubmed:37202450	Mtz Replicate2	GSM6658006	source name:eye\|tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:24h Mtz to ablate rods 24h recovery before collection\|age:7dpf	Mtz Replicate2	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 “cat” 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’s 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	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	tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:24h Mtz to ablate rods 24h recovery before collection\|age:7dpf	GSM6658006	GSM6658006: Mtz Replicate2; Danio rerio; RNA Seq	GSM6658006 r1	GSM6658006	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	loader:fastq load.py	KEmm-Mtz-2_S2_L001_R1_001.fastq.gz	fastq	2715374800.0	27153748.0	GSM6658006 r1	0:100	A:728944098;C:632738961;G:611124541;T:742478488;N:88712	100	728944098	632738961	611124541	742478488	88712	SRX17949911	SRS15467386	SRA1524004	Mumm lab, Human Genetics, Johns Hopkins University	Mumm lab, Human Genetics, Johns Hopkins University	1	0.92125	0.1561	0.69349	0.42881	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71752	71752	SRR21966441	SRX17949911	SRS15467386	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	pubmed:37202450	Mtz Replicate2	GSM6658006	source name:eye\|tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:24h Mtz to ablate rods 24h recovery before collection\|age:7dpf	Mtz Replicate2	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 “cat” 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’s 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	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	tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:24h Mtz to ablate rods 24h recovery before collection\|age:7dpf	GSM6658006	GSM6658006: Mtz Replicate2; Danio rerio; RNA Seq	GSM6658006 r1	GSM6658006	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	loader:fastq load.py	KEmm-Mtz-2_S2_L002_R1_001.fastq.gz	fastq	2796233600.0	27962336.0	GSM6658006 r2	0:100	A:751284801;C:651629570;G:628368568;T:764879710;N:70951	100	751284801	651629570	628368568	764879710	70951	SRX17949911	SRS15467386	SRA1524004	Mumm lab, Human Genetics, Johns Hopkins University	Mumm lab, Human Genetics, Johns Hopkins University	1	0.91823	0.1555	0.69114	0.43015	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71753	71753	SRR21966442	SRX17949910	SRS15467385	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	pubmed:37202450	Mtz Replicate1	GSM6658005	source name:eye\|tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:24h Mtz to ablate rods 24h recovery before collection\|age:7dpf	Mtz 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 “cat” 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’s 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	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	tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:24h Mtz to ablate rods 24h recovery before collection\|age:7dpf	GSM6658005	GSM6658005: Mtz Replicate1; Danio rerio; RNA Seq	GSM6658005 r1	GSM6658005	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	loader:fastq load.py	KEmm-Mtz-1_S1_L001_R1_001.fastq.gz	fastq	2991948800.0	29919488.0	GSM6658005 r1	0:100	A:803050806;C:710041300;G:663800806;T:814960172;N:95716	100	803050806	710041300	663800806	814960172	95716	SRX17949910	SRS15467385	SRA1524004	Mumm lab, Human Genetics, Johns Hopkins University	Mumm lab, Human Genetics, Johns Hopkins University	1	0.92142	0.15558	0.69493	0.43229	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System
71754	71754	SRR21966443	SRX17949910	SRS15467385	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	pubmed:37202450	Mtz Replicate1	GSM6658005	source name:eye\|tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:24h Mtz to ablate rods 24h recovery before collection\|age:7dpf	Mtz 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 “cat” 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’s 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	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	tissue:eye\|genotype:Tgrho:YFP Eco. NfsBgmc500\|treatment:24h Mtz to ablate rods 24h recovery before collection\|age:7dpf	GSM6658005	GSM6658005: Mtz Replicate1; Danio rerio; RNA Seq	GSM6658005 r1	GSM6658005	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP403311	loader:fastq load.py	KEmm-Mtz-1_S1_L002_R1_001.fastq.gz	fastq	3048272600.0	30482726.0	GSM6658005 r2	0:100	A:818711227;C:723604266;G:675169667;T:830712010;N:75430	100	818711227	723604266	675169667	830712010	75430	SRX17949910	SRS15467385	SRA1524004	Mumm lab, Human Genetics, Johns Hopkins University	Mumm lab, Human Genetics, Johns Hopkins University	1	0.92156	0.15547	0.69418	0.43631	100	B	usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk	United States	2022-10-18	Larval	Larval	Eye	Sensory System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;