metadata: run_metadata: 589 rows where devstage_curation_coarse = "Larval" and tissue_curation

589 rows where devstage_curation_coarse = "Larval" and tissue_curation_coarse = "Sensory System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.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.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
10155	10155	ERR5236196	ERX5039563	ERS5672247	ERP126773	PRJEB42852	RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	E-MTAB-10068	Transcriptome Analysis	Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure.	ENA FIRST PUBLIC:2022 01 26\|ENA LAST UPDATE:2022 01 26		Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E.	Zebrafish WT 3	SAMEA7984965	Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA	ENA first public:2022 01 26\|ENA last update:2022 01 26\|External Id:SAMEA7984965\|INSDC center alias:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA\|INSDC center name:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA\|INSDC first public:2022 01 26T00:16:15Z\|INSDC last update:2022 01 26T00:16:15Z\|INSDC status:public\|Submitter Id:E MTAB 10068:Zebrafish WT 3\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:late embryonic stage\|genotype:wild type genotype\|organism part:eye\|sample name:E MTAB 10068:Zebrafish WT 3							Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	E MTAB 10068:Zebrafish WT 3 p	Zebrafish WT 3 p	RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E.	Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP126773	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	ENA FIRST PUBLIC:2022 01 26\|ENA LAST UPDATE:2022 01 26	Zebrafish_WT_3_1.fastq.gz Zebrafish_WT_3_2.fastq.gz	fastq fastq	7150981594.0	23678747.0	E MTAB 10068:Zebrafish WT 3	0:151 1:151	A:1885053833;C:1690814929;G:1772259046;T:1802798453;N:55333	151	151	1885053833	1690814929	1772259046	1802798453	55333	ERX5039563	ERS5672247	ERA3400155	Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA\|European Nucleotide Archive	Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA\|European Nucleotide Archive	2	0.95124	0.95221	0.08338	0.08285	0.69181	0.69256	0.46157	0.46139	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2022-01-26	Larval	Larval	Eye	Sensory System
10156	10156	ERR5236195	ERX5039562	ERS5672246	ERP126773	PRJEB42852	RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	E-MTAB-10068	Transcriptome Analysis	Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure.	ENA FIRST PUBLIC:2022 01 26\|ENA LAST UPDATE:2022 01 26		Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E.	Zebrafish WT 2	SAMEA7984964	Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA	ENA first public:2022 01 26\|ENA last update:2022 01 26\|External Id:SAMEA7984964\|INSDC center alias:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA\|INSDC center name:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA\|INSDC first public:2022 01 26T00:16:15Z\|INSDC last update:2022 01 26T00:16:15Z\|INSDC status:public\|Submitter Id:E MTAB 10068:Zebrafish WT 2\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:late embryonic stage\|genotype:wild type genotype\|organism part:eye\|sample name:E MTAB 10068:Zebrafish WT 2							Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	E MTAB 10068:Zebrafish WT 2 p	Zebrafish WT 2 p	RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E.	Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP126773	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	ENA FIRST PUBLIC:2022 01 26\|ENA LAST UPDATE:2022 01 26	Zebrafish_WT_2_1.fastq.gz Zebrafish_WT_2_2.fastq.gz	fastq fastq	7214044026.0	23887563.0	E MTAB 10068:Zebrafish WT 2	0:151 1:151	A:1902219751;C:1705162605;G:1795933407;T:1810669383;N:58880	151	151	1902219751	1705162605	1795933407	1810669383	58880	ERX5039562	ERS5672246	ERA3400155	Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA\|European Nucleotide Archive	Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA\|European Nucleotide Archive	2	0.95311	0.95386	0.07898	0.07845	0.69045	0.69061	0.46066	0.4628	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2022-01-26	Larval	Larval	Eye	Sensory System
10157	10157	ERR5236194	ERX5039561	ERS5672245	ERP126773	PRJEB42852	RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	E-MTAB-10068	Transcriptome Analysis	Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure.	ENA FIRST PUBLIC:2022 01 26\|ENA LAST UPDATE:2022 01 26		Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E.	Zebrafish WT 1	SAMEA7984963	Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA	ENA first public:2022 01 26\|ENA last update:2022 01 26\|External Id:SAMEA7984963\|INSDC center alias:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA\|INSDC center name:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA\|INSDC first public:2022 01 26T00:16:15Z\|INSDC last update:2022 01 26T00:16:15Z\|INSDC status:public\|Submitter Id:E MTAB 10068:Zebrafish WT 1\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:late embryonic stage\|genotype:wild type genotype\|organism part:eye\|sample name:E MTAB 10068:Zebrafish WT 1							Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	E MTAB 10068:Zebrafish WT 1 p	Zebrafish WT 1 p	RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E.	Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP126773	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	ENA FIRST PUBLIC:2022 01 26\|ENA LAST UPDATE:2022 01 26	Zebrafish_WT_1_1.fastq.gz Zebrafish_WT_1_2.fastq.gz	fastq fastq	6632043216.0	21960408.0	E MTAB 10068:Zebrafish WT 1	0:151 1:151	A:1763732625;C:1547925091;G:1636588945;T:1683739270;N:57285	151	151	1763732625	1547925091	1636588945	1683739270	57285	ERX5039561	ERS5672245	ERA3400155	Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA\|European Nucleotide Archive	Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA\|European Nucleotide Archive	2	0.9495	0.95025	0.08958	0.08856	0.68661	0.68598	0.46029	0.46171	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2022-01-26	Larval	Larval	Eye	Sensory System
10158	10158	ERR5236193	ERX5039560	ERS5672244	ERP126773	PRJEB42852	RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	E-MTAB-10068	Transcriptome Analysis	Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure.	ENA FIRST PUBLIC:2022 01 26\|ENA LAST UPDATE:2022 01 26		Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E.	Zebrafish mab21l1 3	SAMEA7984962	Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA	ENA first public:2022 01 26\|ENA last update:2022 01 26\|External Id:SAMEA7984962\|INSDC center alias:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA\|INSDC center name:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA\|INSDC first public:2022 01 26T00:16:15Z\|INSDC last update:2022 01 26T00:16:15Z\|INSDC status:public\|Submitter Id:E MTAB 10068:Zebrafish mab21l1 3\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:late embryonic stage\|genotype:homozygous mab21l1 c.107delA\|organism part:eye\|sample name:E MTAB 10068:Zebrafish mab21l1 3							Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	E MTAB 10068:Zebrafish mab21l1 3 p	Zebrafish mab21l1 3 p	RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E.	Experimental Factor: genotype:homozygous mab21l1 c.107delA	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP126773	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	ENA FIRST PUBLIC:2022 01 26\|ENA LAST UPDATE:2022 01 26	Zebrafish_mab21l1_3_1.fastq.gz Zebrafish_mab21l1_3_2.fastq.gz	fastq fastq	6182833618.0	20472959.0	E MTAB 10068:Zebrafish mab21l1 3	0:151 1:151	A:1613191835;C:1471874932;G:1547131522;T:1550575662;N:59667	151	151	1613191835	1471874932	1547131522	1550575662	59667	ERX5039560	ERS5672244	ERA3400155	Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA\|European Nucleotide Archive	Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA\|European Nucleotide Archive	2	0.95645	0.95788	0.0697	0.06969	0.70096	0.70033	0.43342	0.43242	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2022-01-26	Larval	Larval	Eye	Sensory System
10159	10159	ERR5236192	ERX5039559	ERS5672243	ERP126773	PRJEB42852	RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	E-MTAB-10068	Transcriptome Analysis	Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure.	ENA FIRST PUBLIC:2022 01 26\|ENA LAST UPDATE:2022 01 26		Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E.	Zebrafish mab21l1 2	SAMEA7984961	Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA	ENA first public:2022 01 26\|ENA last update:2022 01 26\|External Id:SAMEA7984961\|INSDC center alias:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA\|INSDC center name:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA\|INSDC first public:2022 01 26T00:16:15Z\|INSDC last update:2022 01 26T00:16:15Z\|INSDC status:public\|Submitter Id:E MTAB 10068:Zebrafish mab21l1 2\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:late embryonic stage\|genotype:homozygous mab21l1 c.107delA\|organism part:eye\|sample name:E MTAB 10068:Zebrafish mab21l1 2							Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	E MTAB 10068:Zebrafish mab21l1 2 p	Zebrafish mab21l1 2 p	RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E.	Experimental Factor: genotype:homozygous mab21l1 c.107delA	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP126773	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	ENA FIRST PUBLIC:2022 01 26\|ENA LAST UPDATE:2022 01 26	Zebrafish_mab21l1_2_1.fastq.gz Zebrafish_mab21l1_2_2.fastq.gz	fastq fastq	6989382602.0	23143651.0	E MTAB 10068:Zebrafish mab21l1 2	0:151 1:151	A:1841093814;C:1660652130;G:1754262273;T:1733319973;N:54412	151	151	1841093814	1660652130	1754262273	1733319973	54412	ERX5039559	ERS5672243	ERA3400155	Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA\|European Nucleotide Archive	Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA\|European Nucleotide Archive	2	0.95595	0.95712	0.07199	0.07107	0.70485	0.70431	0.42033	0.42681	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2022-01-26	Larval	Larval	Eye	Sensory System
10160	10160	ERR5236191	ERX5039558	ERS5672242	ERP126773	PRJEB42852	RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	E-MTAB-10068	Transcriptome Analysis	Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure.	ENA FIRST PUBLIC:2022 01 26\|ENA LAST UPDATE:2022 01 26		Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E.	Zebrafish mab21l1 1	SAMEA7984960	Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA	ENA first public:2022 01 26\|ENA last update:2022 01 26\|External Id:SAMEA7984960\|INSDC center alias:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA\|INSDC center name:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA\|INSDC first public:2022 01 26T00:16:15Z\|INSDC last update:2022 01 26T00:16:15Z\|INSDC status:public\|Submitter Id:E MTAB 10068:Zebrafish mab21l1 1\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:late embryonic stage\|genotype:homozygous mab21l1 c.107delA\|organism part:eye\|sample name:E MTAB 10068:Zebrafish mab21l1 1							Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	E MTAB 10068:Zebrafish mab21l1 1 p	Zebrafish mab21l1 1 p	RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E.	Experimental Factor: genotype:homozygous mab21l1 c.107delA	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP126773	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf	ENA FIRST PUBLIC:2022 01 26\|ENA LAST UPDATE:2022 01 26	Zebrafish_mab21l1_1_1.fastq.gz Zebrafish_mab21l1_1_2.fastq.gz	fastq fastq	6882371922.0	22789311.0	E MTAB 10068:Zebrafish mab21l1 1	0:151 1:151	A:1803380739;C:1630414039;G:1732263332;T:1716255495;N:58317	151	151	1803380739	1630414039	1732263332	1716255495	58317	ERX5039558	ERS5672242	ERA3400155	Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA\|European Nucleotide Archive	Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA\|European Nucleotide Archive	2	0.95518	0.95612	0.07088	0.07032	0.70526	0.70457	0.42942	0.4302	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2022-01-26	Larval	Larval	Eye	Sensory System
29107	29107	SRR27151543	SRX22833143	SRS19813583	SRP476691	PRJNA1050282	Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf whole eye]	GSE249751	Transcriptome Analysis	The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces.	parent bioproject:PRJNA1050288	pubmed:39531499		5 dpf larval eyes samd7 / rep3	GSM7963641		source name:eye\|tissue:eye\|developmental stage:5 dpf larvae\|genotype:samd7 / \|geo loc name:missing\|collection date:missing	5 dpf larval eyes samd7 / rep3	Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf larval eyes. Genes are ranked by p adj.	eye	To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.	tissue:eye\|developmental stage:5 dpf larvae\|genotype:samd7 /	GSM7963641	GSM7963641: 5 dpf larval eyes samd7 / rep3; Danio rerio; RNA Seq	GSM7963641 r1	GSM7963641	1	To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP476691		loader:fastq load.py	k7.AGGTATTCGG-GAGTCGCTTC.H37F5DSX2_AGGTATTCGG-GAGTCGCTTC_L003_R1.fastq.gz k7.AGGTATTCGG-GAGTCGCTTC.H37F5DSX2_AGGTATTCGG-GAGTCGCTTC_L003_R2.fastq.gz	fastq fastq	10747100652.0	35586426.0	GSM7963641 r1	0:151 1:151	A:2879574125;C:2414500329;G:2693618198;T:2759237631;N:170369	151	151	2879574125	2414500329	2693618198	2759237631	170369	SRX22833143	SRS19813583	SRA1765718	Pathology and Immunology, Washington University School of Medicine	Pathology and Immunology, Washington University School of Medicine	2	0.95486	0.95989	0.05038	0.05167	0.73018	0.73438	0.41476	0.42743	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	random_priming	smarter	bulk	unknown	unknown	United States	2023-12-08	Larval	Larval	Eye	Sensory System
29108	29108	SRR27151544	SRX22833142	SRS19813582	SRP476691	PRJNA1050282	Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf whole eye]	GSE249751	Transcriptome Analysis	The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces.	parent bioproject:PRJNA1050288	pubmed:39531499		5 dpf larval eyes samd7 / rep2	GSM7963640		source name:eye\|tissue:eye\|developmental stage:5 dpf larvae\|genotype:samd7 / \|geo loc name:missing\|collection date:missing	5 dpf larval eyes samd7 / rep2	Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf larval eyes. Genes are ranked by p adj.	eye	To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.	tissue:eye\|developmental stage:5 dpf larvae\|genotype:samd7 /	GSM7963640	GSM7963640: 5 dpf larval eyes samd7 / rep2; Danio rerio; RNA Seq	GSM7963640 r1	GSM7963640	1	To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP476691		loader:fastq load.py	k10.AATCGAACTC-TTAGACCTTC.H37F5DSX2_AATCGAACTC-TTAGACCTTC_L003_R1.fastq.gz k10.AATCGAACTC-TTAGACCTTC.H37F5DSX2_AATCGAACTC-TTAGACCTTC_L003_R2.fastq.gz	fastq fastq	10739126946.0	35560023.0	GSM7963640 r1	0:151 1:151	A:2888527520;C:2418475992;G:2670968816;T:2760983764;N:170854	151	151	2888527520	2418475992	2670968816	2760983764	170854	SRX22833142	SRS19813582	SRA1765718	Pathology and Immunology, Washington University School of Medicine	Pathology and Immunology, Washington University School of Medicine	2	0.95306	0.95846	0.05658	0.05746	0.73269	0.73714	0.42191	0.43088	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	random_priming	smarter	bulk	unknown	unknown	United States	2023-12-08	Larval	Larval	Eye	Sensory System
29109	29109	SRR27151545	SRX22833141	SRS19813581	SRP476691	PRJNA1050282	Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf whole eye]	GSE249751	Transcriptome Analysis	The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces.	parent bioproject:PRJNA1050288	pubmed:39531499		5 dpf larval eyes samd7 / rep1	GSM7963639		source name:eye\|tissue:eye\|developmental stage:5 dpf larvae\|genotype:samd7 / \|geo loc name:missing\|collection date:missing	5 dpf larval eyes samd7 / rep1	Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf larval eyes. Genes are ranked by p adj.	eye	To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.	tissue:eye\|developmental stage:5 dpf larvae\|genotype:samd7 /	GSM7963639	GSM7963639: 5 dpf larval eyes samd7 / rep1; Danio rerio; RNA Seq	GSM7963639 r1	GSM7963639	1	To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP476691		loader:fastq load.py	k11.CCGAAGATAA-TGGATTAACG.H37F5DSX2_CCGAAGATAA-TGGATTAACG_L003_R1.fastq.gz k11.CCGAAGATAA-TGGATTAACG.H37F5DSX2_CCGAAGATAA-TGGATTAACG_L003_R2.fastq.gz	fastq fastq	10514289154.0	34815527.0	GSM7963639 r1	0:151 1:151	A:2862247233;C:2377266250;G:2528917605;T:2745692826;N:165240	151	151	2862247233	2377266250	2528917605	2745692826	165240	SRX22833141	SRS19813581	SRA1765718	Pathology and Immunology, Washington University School of Medicine	Pathology and Immunology, Washington University School of Medicine	2	0.95376	0.95966	0.05526	0.05681	0.72965	0.73273	0.42276	0.43148	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	random_priming	smarter	bulk	unknown	unknown	United States	2023-12-08	Larval	Larval	Eye	Sensory System
29110	29110	SRR27151546	SRX22833140	SRS19813578	SRP476691	PRJNA1050282	Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf whole eye]	GSE249751	Transcriptome Analysis	The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces.	parent bioproject:PRJNA1050288	pubmed:39531499		5 dpf larval eyes WT rep3	GSM7963638		source name:eye\|tissue:eye\|developmental stage:5 dpf larvae\|genotype:WT\|geo loc name:missing\|collection date:missing	5 dpf larval eyes WT rep3	Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf larval eyes. Genes are ranked by p adj.	eye	To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.	tissue:eye\|developmental stage:5 dpf larvae\|genotype:WT	GSM7963638	GSM7963638: 5 dpf larval eyes WT rep3; Danio rerio; RNA Seq	GSM7963638 r1	GSM7963638	1	To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP476691		loader:fastq load.py	w6.CCTTGCCGTA-TAGTACACAG.H37F5DSX2_CCTTGCCGTA-TAGTACACAG_L003_R1.fastq.gz w6.CCTTGCCGTA-TAGTACACAG.H37F5DSX2_CCTTGCCGTA-TAGTACACAG_L003_R2.fastq.gz	fastq fastq	11943994904.0	39549652.0	GSM7963638 r1	0:151 1:151	A:3182349655;C:2708994785;G:2976982793;T:3075478468;N:189203	151	151	3182349655	2708994785	2976982793	3075478468	189203	SRX22833140	SRS19813578	SRA1765718	Pathology and Immunology, Washington University School of Medicine	Pathology and Immunology, Washington University School of Medicine	2	0.95522	0.96109	0.04859	0.04955	0.74247	0.74799	0.42424	0.43226	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	random_priming	smarter	bulk	unknown	unknown	United States	2023-12-08	Larval	Larval	Eye	Sensory System
29111	29111	SRR27151547	SRX22833139	SRS19813579	SRP476691	PRJNA1050282	Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf whole eye]	GSE249751	Transcriptome Analysis	The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces.	parent bioproject:PRJNA1050288	pubmed:39531499		5 dpf larval eyes WT rep2	GSM7963637		source name:eye\|tissue:eye\|developmental stage:5 dpf larvae\|genotype:WT\|geo loc name:missing\|collection date:missing	5 dpf larval eyes WT rep2	Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf larval eyes. Genes are ranked by p adj.	eye	To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.	tissue:eye\|developmental stage:5 dpf larvae\|genotype:WT	GSM7963637	GSM7963637: 5 dpf larval eyes WT rep2; Danio rerio; RNA Seq	GSM7963637 r1	GSM7963637	1	To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP476691		loader:fastq load.py	w8.AATCTCAGGC-TCACCAGGAC.H37F5DSX2_AATCTCAGGC-TCACCAGGAC_L003_R1.fastq.gz w8.AATCTCAGGC-TCACCAGGAC.H37F5DSX2_AATCTCAGGC-TCACCAGGAC_L003_R2.fastq.gz	fastq fastq	10471048190.0	34672345.0	GSM7963637 r1	0:151 1:151	A:2767212261;C:2402799397;G:2644524852;T:2656347723;N:163957	151	151	2767212261	2402799397	2644524852	2656347723	163957	SRX22833139	SRS19813579	SRA1765718	Pathology and Immunology, Washington University School of Medicine	Pathology and Immunology, Washington University School of Medicine	2	0.95909	0.96443	0.04132	0.04289	0.74217	0.74631	0.40379	0.41076	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	random_priming	smarter	bulk	unknown	unknown	United States	2023-12-08	Larval	Larval	Eye	Sensory System
29112	29112	SRR27151548	SRX22833138	SRS19813580	SRP476691	PRJNA1050282	Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf whole eye]	GSE249751	Transcriptome Analysis	The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces.	parent bioproject:PRJNA1050288	pubmed:39531499		5 dpf larval eyes WT rep1	GSM7963636		source name:eye\|tissue:eye\|developmental stage:5 dpf larvae\|genotype:WT\|geo loc name:missing\|collection date:missing	5 dpf larval eyes WT rep1	Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf larval eyes. Genes are ranked by p adj.	eye	To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.	tissue:eye\|developmental stage:5 dpf larvae\|genotype:WT	GSM7963636	GSM7963636: 5 dpf larval eyes WT rep1; Danio rerio; RNA Seq	GSM7963636 r1	GSM7963636	1	To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP476691		loader:fastq load.py	w15.AACAGGCAAG-TTCATGGAAG.H37F5DSX2_AACAGGCAAG-TTCATGGAAG_L003_R1.fastq.gz w15.AACAGGCAAG-TTCATGGAAG.H37F5DSX2_AACAGGCAAG-TTCATGGAAG_L003_R2.fastq.gz	fastq fastq	11852131940.0	39245470.0	GSM7963636 r1	0:151 1:151	A:3157263060;C:2691924686;G:2998627934;T:3004129760;N:186500	151	151	3157263060	2691924686	2998627934	3004129760	186500	SRX22833138	SRS19813580	SRA1765718	Pathology and Immunology, Washington University School of Medicine	Pathology and Immunology, Washington University School of Medicine	2	0.95652	0.96043	0.05012	0.05113	0.73198	0.73637	0.42361	0.41636	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	random_priming	smarter	bulk	unknown	unknown	United States	2023-12-08	Larval	Larval	Eye	Sensory System
29119	29119	SRR27151354	SRX22832956	SRS19813396	SRP476687	PRJNA1050291	Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf td]	GSE249755	Transcriptome Analysis	The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS as described in another section. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4.	parent bioproject:PRJNA1050288	pubmed:39531499		thrb:tdTomato+ cells from 5 dpf larval eyes samd7 / rep3	GSM7963660		source name:eye\|cell type:thrb:tdTomato+ cells\|tissue:eye\|developmental stage:5 dpf larvae\|genotype:samd7 / \|geo loc name:missing\|collection date:missing	thrb:tdTomato+ cells from 5 dpf larval eyes samd7 / rep3	Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf thrb:tdTomato+ cells. Genes are ranked by p adj.	eye	To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.	cell type:thrb:tdTomato+ cells\|tissue:eye\|developmental stage:5 dpf larvae\|genotype:samd7 /	GSM7963660	GSM7963660: thrb:tdTomato+ cells from 5 dpf larval eyes samd7 / rep3; Danio rerio; RNA Seq	GSM7963660 r1	GSM7963660	1	To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP476687		loader:fastq load.py	samd7_1_rna_6_2_22.AGAAGGAACA-TGGTAGATGC.HNGJJDSX3_AGAAGGAACA-TGGTAGATGC_L003_R1.fastq.gz samd7_1_rna_6_2_22.AGAAGGAACA-TGGTAGATGC.HNGJJDSX3_AGAAGGAACA-TGGTAGATGC_L003_R2.fastq.gz	fastq fastq	10483631624.0	34714012.0	GSM7963660 r1	0:151 1:151	A:2778161057;C:2394557806;G:2692864342;T:2618022344;N:26075	151	151	2778161057	2394557806	2692864342	2618022344	26075	SRX22832956	SRS19813396	SRA1765707	Pathology and Immunology, Washington University School of Medicine	Pathology and Immunology, Washington University School of Medicine	2	0.91943	0.91641	0.08589	0.08581	0.78748	0.79774	0.5086	0.50263	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2023-12-08	Larval	Larval	Eye	Sensory System
29120	29120	SRR27151355	SRX22832955	SRS19813395	SRP476687	PRJNA1050291	Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf td]	GSE249755	Transcriptome Analysis	The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS as described in another section. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4.	parent bioproject:PRJNA1050288	pubmed:39531499		thrb:tdTomato+ cells from 5 dpf larval eyes samd7 / rep2	GSM7963659		source name:eye\|cell type:thrb:tdTomato+ cells\|tissue:eye\|developmental stage:5 dpf larvae\|genotype:samd7 / \|geo loc name:missing\|collection date:missing	thrb:tdTomato+ cells from 5 dpf larval eyes samd7 / rep2	Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf thrb:tdTomato+ cells. Genes are ranked by p adj.	eye	To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.	cell type:thrb:tdTomato+ cells\|tissue:eye\|developmental stage:5 dpf larvae\|genotype:samd7 /	GSM7963659	GSM7963659: thrb:tdTomato+ cells from 5 dpf larval eyes samd7 / rep2; Danio rerio; RNA Seq	GSM7963659 r1	GSM7963659	1	To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP476687		loader:fastq load.py	samd7_1_rna_6_1_22.AGACAGACGT-TATCAGTGCA.HNGJJDSX3_AGACAGACGT-TATCAGTGCA_L003_R1.fastq.gz samd7_1_rna_6_1_22.AGACAGACGT-TATCAGTGCA.HNGJJDSX3_AGACAGACGT-TATCAGTGCA_L003_R2.fastq.gz	fastq fastq	12234446424.0	40511412.0	GSM7963659 r1	0:151 1:151	A:3397427491;C:2650252489;G:2963872812;T:3222862933;N:30699	151	151	3397427491	2650252489	2963872812	3222862933	30699	SRX22832955	SRS19813395	SRA1765707	Pathology and Immunology, Washington University School of Medicine	Pathology and Immunology, Washington University School of Medicine	2	0.89702	0.8967	0.14358	0.14658	0.77309	0.77962	0.5468	0.44645	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2023-12-08	Larval	Larval	Eye	Sensory System
29121	29121	SRR27151356	SRX22832954	SRS19813394	SRP476687	PRJNA1050291	Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf td]	GSE249755	Transcriptome Analysis	The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS as described in another section. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4.	parent bioproject:PRJNA1050288	pubmed:39531499		thrb:tdTomato+ cells from 5 dpf larval eyes samd7 / rep1	GSM7963658		source name:eye\|cell type:thrb:tdTomato+ cells\|tissue:eye\|developmental stage:5 dpf larvae\|genotype:samd7 / \|geo loc name:missing\|collection date:missing	thrb:tdTomato+ cells from 5 dpf larval eyes samd7 / rep1	Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf thrb:tdTomato+ cells. Genes are ranked by p adj.	eye	To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.	cell type:thrb:tdTomato+ cells\|tissue:eye\|developmental stage:5 dpf larvae\|genotype:samd7 /	GSM7963658	GSM7963658: thrb:tdTomato+ cells from 5 dpf larval eyes samd7 / rep1; Danio rerio; RNA Seq	GSM7963658 r1	GSM7963658	1	To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP476687		loader:fastq load.py	samd7_rna_5_10_22.CAATTCACGC-ACATCCTGCG.HNGJJDSX3_CAATTCACGC-ACATCCTGCG_L003_R1.fastq.gz samd7_rna_5_10_22.CAATTCACGC-ACATCCTGCG.HNGJJDSX3_CAATTCACGC-ACATCCTGCG_L003_R2.fastq.gz	fastq fastq	11352128660.0	37589830.0	GSM7963658 r1	0:151 1:151	A:3035915425;C:2447970512;G:2970538003;T:2897676299;N:28421	151	151	3035915425	2447970512	2970538003	2897676299	28421	SRX22832954	SRS19813394	SRA1765707	Pathology and Immunology, Washington University School of Medicine	Pathology and Immunology, Washington University School of Medicine	2	0.90706	0.91061	0.09833	0.102	0.78186	0.78948	0.54785	0.47215	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2023-12-08	Larval	Larval	Eye	Sensory System
29122	29122	SRR27151357	SRX22832953	SRS19813393	SRP476687	PRJNA1050291	Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf td]	GSE249755	Transcriptome Analysis	The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS as described in another section. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4.	parent bioproject:PRJNA1050288	pubmed:39531499		thrb:tdTomato+ cells from 5 dpf larval eyes WT rep3	GSM7963657		source name:eye\|cell type:thrb:tdTomato+ cells\|tissue:eye\|developmental stage:5 dpf larvae\|genotype:WT\|geo loc name:missing\|collection date:missing	thrb:tdTomato+ cells from 5 dpf larval eyes WT rep3	Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf thrb:tdTomato+ cells. Genes are ranked by p adj.	eye	To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.	cell type:thrb:tdTomato+ cells\|tissue:eye\|developmental stage:5 dpf larvae\|genotype:WT	GSM7963657	GSM7963657: thrb:tdTomato+ cells from 5 dpf larval eyes WT rep3; Danio rerio; RNA Seq	GSM7963657 r1	GSM7963657	1	To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP476687		loader:fastq load.py	wt_3_a_rna_5_12_22.CACCATTGTA-TACCAATTGC.HNGJJDSX3_CACCATTGTA-TACCAATTGC_L003_R1.fastq.gz wt_3_a_rna_5_12_22.CACCATTGTA-TACCAATTGC.HNGJJDSX3_CACCATTGTA-TACCAATTGC_L003_R2.fastq.gz	fastq fastq	9723911364.0	32198382.0	GSM7963657 r1	0:151 1:151	A:2610813507;C:2104688166;G:2520224929;T:2488160661;N:24101	151	151	2610813507	2104688166	2520224929	2488160661	24101	SRX22832953	SRS19813393	SRA1765707	Pathology and Immunology, Washington University School of Medicine	Pathology and Immunology, Washington University School of Medicine	2	0.62594	0.60745	0.07012	0.07039	0.81728	0.82578	0.50983	0.57347	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2023-12-08	Larval	Larval	Eye	Sensory System
29123	29123	SRR27151358	SRX22832952	SRS19813392	SRP476687	PRJNA1050291	Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf td]	GSE249755	Transcriptome Analysis	The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS as described in another section. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4.	parent bioproject:PRJNA1050288	pubmed:39531499		thrb:tdTomato+ cells from 5 dpf larval eyes WT rep2	GSM7963656		source name:eye\|cell type:thrb:tdTomato+ cells\|tissue:eye\|developmental stage:5 dpf larvae\|genotype:WT\|geo loc name:missing\|collection date:missing	thrb:tdTomato+ cells from 5 dpf larval eyes WT rep2	Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf thrb:tdTomato+ cells. Genes are ranked by p adj.	eye	To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.	cell type:thrb:tdTomato+ cells\|tissue:eye\|developmental stage:5 dpf larvae\|genotype:WT	GSM7963656	GSM7963656: thrb:tdTomato+ cells from 5 dpf larval eyes WT rep2; Danio rerio; RNA Seq	GSM7963656 r1	GSM7963656	1	To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP476687		loader:fastq load.py	wt_2_b_rna_5_12_22.AAGACTCTCG-TAAGTCTGGC.HNGJJDSX3_AAGACTCTCG-TAAGTCTGGC_L003_R1.fastq.gz wt_2_b_rna_5_12_22.AAGACTCTCG-TAAGTCTGGC.HNGJJDSX3_AAGACTCTCG-TAAGTCTGGC_L003_R2.fastq.gz	fastq fastq	10722667946.0	35505523.0	GSM7963656 r1	0:151 1:151	A:2872256957;C:2358147851;G:2771142656;T:2721093653;N:26829	151	151	2872256957	2358147851	2771142656	2721093653	26829	SRX22832952	SRS19813392	SRA1765707	Pathology and Immunology, Washington University School of Medicine	Pathology and Immunology, Washington University School of Medicine	2	0.90028	0.8986	0.10012	0.10225	0.7973	0.80389	0.56209	0.56007	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2023-12-08	Larval	Larval	Eye	Sensory System
29124	29124	SRR27151359	SRX22832951	SRS19813391	SRP476687	PRJNA1050291	Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf td]	GSE249755	Transcriptome Analysis	The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS as described in another section. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4.	parent bioproject:PRJNA1050288	pubmed:39531499		thrb:tdTomato+ cells from 5 dpf larval eyes WT rep1	GSM7963655		source name:eye\|cell type:thrb:tdTomato+ cells\|tissue:eye\|developmental stage:5 dpf larvae\|genotype:WT\|geo loc name:missing\|collection date:missing	thrb:tdTomato+ cells from 5 dpf larval eyes WT rep1	Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf thrb:tdTomato+ cells. Genes are ranked by p adj.	eye	To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.	cell type:thrb:tdTomato+ cells\|tissue:eye\|developmental stage:5 dpf larvae\|genotype:WT	GSM7963655	GSM7963655: thrb:tdTomato+ cells from 5 dpf larval eyes WT rep1; Danio rerio; RNA Seq	GSM7963655 r1	GSM7963655	1	To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP476687		loader:fastq load.py	wt_rna_5_10_22.CCACCTTCAA-ACCATCGAGG.HNGJJDSX3_CCACCTTCAA-ACCATCGAGG_L003_R1.fastq.gz wt_rna_5_10_22.CCACCTTCAA-ACCATCGAGG.HNGJJDSX3_CCACCTTCAA-ACCATCGAGG_L003_R2.fastq.gz	fastq fastq	9875387618.0	32699959.0	GSM7963655 r1	0:151 1:151	A:2640364023;C:2083842037;G:2621465276;T:2529691405;N:24877	151	151	2640364023	2083842037	2621465276	2529691405	24877	SRX22832951	SRS19813391	SRA1765707	Pathology and Immunology, Washington University School of Medicine	Pathology and Immunology, Washington University School of Medicine	2	0.90131	0.90429	0.10837	0.1106	0.79523	0.80182	0.50934	0.58039	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2023-12-08	Larval	Larval	Eye	Sensory System
29174	29174	SRR27237224	SRX22915658	SRS19883761	SRP478464	PRJNA1053781	Single cell gene expression profie of developing photoreceptor cells in larval zebrafish	GSE250379	Other	Molecular underpinnings of vertebrate retinal differentiation and maturation are poorly understood particularly for non mammalian species. We generated single cell transcriptome data from the larval zebrafish retina and characterized gene expression diversity among photoreceptor subtypes and their progenitors. Overall design: GFP positive differentiating photoreceptor cells and bipolar cells were collected from 4 dpf larval transgenic zebrafish Tgcrx:EGFPstl887 using fluorescence activated cell sorting.	parent bioproject:PRJNA1050288	pubmed:39531499		retina scRNA seq	GSM7978132		source name:retina\|tissue:retina\|genotype:Tgcrx:EGFPstl887\|developmental stage:4 dpf\|geo loc name:missing\|collection date:missing	retina scRNA seq	Read alignment and initial quality control were performed using Cell Ranger software version 7.0.0 10X Genomics. Assembly: GRCz11 Supplementary files format and content: Tab separated value file and matrix file	retina	Fifty heads were dissected from 4 dpf heterozygous Tgcrx:GFPstl887Tg larvae. Following dissection eyes were stored in ice cold Hanks’ Balanced Salt Solution HBSS until all eyes were harvested. Once the eyes were collected HBSS was removed and the eyes were incubated in 400 µl of calcium/magnesium free HBSS containing 0.4 mg papain Worthington Biochem for 15 min at 37°C. 800 µl of 10% fetal bovine serum FBS in Dulbecco's Modified Eagle Medium DMEM containing 5mM MgCl2 and 120 units DNaseI Roche were added to the mixture and incubated for 5 min at 37°C. Cells were then resuspended in 300 µl of sorting buffer 2.5 mM EDTA 25 mM HEPES 1% bovine serum albumin BSA in calcium/magnesium free HBSS. Cells were sorted on an Aria II FACS machine BD biosciences with gating based on forward scatter side scatter and GFP fluorescence and collected in 700 μl of D PBS without xxx+ and Mg2+ supplemented with 0.4 % BSA D PBS CMF in 1.5 ml microcentrifuge tubes. The collected cells were then centrifuged at 300×g for 5 min washed with D PBS CMF centrifuged and supernatant reduced to 80 µl. Cell density was quantified on a hemocytometer and 5000 cells were used for single cell library preparation. A library for single cell RNA seq was constructed with the Chromium v3 platform 10X Genomics Pleasanton CA according to the manufacturer protocol.	tissue:retina\|genotype:Tgcrx:EGFPstl887\|developmental stage:4 dpf	GSM7978132	GSM7978132: retina scRNA seq; Danio rerio; RNA Seq	GSM7978132 r1	GSM7978132	1	Fifty heads were dissected from 4 dpf heterozygous Tgcrx:GFPstl887Tg larvae. Following dissection eyes were stored in ice cold Hanks' Balanced Salt Solution HBSS until all eyes were harvested. Once the eyes were collected HBSS was removed and the eyes were incubated in 400 µl of calcium/magnesium free HBSS containing 0.4 mg papain Worthington Biochem for 15 min at 37°C. 800 µl of 10% fetal bovine serum FBS in Dulbecco's Modified Eagle Medium DMEM containing 5mM MgCl2 and 120 units DNaseI Roche were added to the mixture and incubated for 5 min at 37°C. Cells were then resuspended in 300 µl of sorting buffer 2.5 mM EDTA 25 mM HEPES 1% bovine serum albumin BSA in calcium/magnesium free HBSS. Cells were sorted on an Aria II FACS machine BD biosciences with gating based on forward scatter side scatter and GFP fluorescence and collected in 700 μl of D PBS without xxx+ and Mg2+ supplemented with 0.4 % BSA D PBS CMF in 1.5 ml microcentrifuge tubes. The collected cells were then centrifuged at 300×g for 5 min washed with D PBS CMF centrifuged and supernatant reduced to 80 µl. Cell density was quantified on a hemocytometer and 5000 cells were used for single cell library preparation. A library for single cell RNA seq was constructed with the Chromium v3 platform 10X Genomics Pleasanton CA according to the manufacturer protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP478464		loader:fastq load.py	crx.crx_S1_L003_R1_001.fastq.gz crx.crx_S1_L003_R2_001.fastq.gz	fastq fastq	45170138494.0	253764823.0	GSM7978132 r1	0:28 1:150	A:13826023801;C:9023674621;G:9590649474;T:12728940802;N:849796	28	150	13826023801	9023674621	9590649474	12728940802	849796	SRX22915658	SRS19883761	SRA1770358	Pathology and Immunology, Washington University School of Medicine	Pathology and Immunology, Washington University School of Medicine	2	0.0046	0.87155	0.00206	0.2263	0.99168	0.77784	0.30223	0.50112	28	150	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-17	Larval	Larval	Eye	Sensory System
31849	31849	SRR28735527	SRX24301508	SRS21065427	SRP502615	PRJNA1101945	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [RNA seq]	GSE264309	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons. The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: AB and double knockout for stim2 stim2a;stim2b / zebrafish 5dpf larvae were used to isolate the total RNA from their eyes. The experimental setup involved 3 replicates per each condition stim2 KO vs control consisting of 35 eyes per repetition.	parent bioproject:PRJNA1101942	pubmed:39424970		stim2KO repllicate 3 RNASeq	GSM8215878		source name:eye\|tissue:eye\|genotype:stim2a;stim2b / \|age:5 dpf\|geo loc name:missing\|collection date:missing	stim2KO repllicate 3 RNASeq	Raw RNA seq data were converted to FASTQ format with bcl2fastq2 v2.17 Illumina and FastQC v0.11.4 was used to assess the quality of each sequencing run. We then utilized the SQuIRE pipeline45 for subsequent steps. STAR version 2.5.3a StringTie version 1.3.3b and DESeq2 version 1.16.149 were used within the SQuIRE pipeline for read alignment transcript assembly and quantification for each replicate and differential gene expression analysis respectively. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated files with raw reads for each sample	eye	Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer’s recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.	tissue:eye\|genotype:stim2a;stim2b / \|age:5 dpf	GSM8215878	GSM8215878: stim2KO repllicate 3 RNASeq; Danio rerio; RNA Seq	GSM8215878 r1	GSM8215878	1	Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer's recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP502615		loader:fastq load.py	mut_rep_3_R1_001.fastq.gz mut_rep_3_R2_001.fastq.gz	fastq fastq	5198552618.0	25735409.0	GSM8215878 r1	0:101 1:101	A:1302884238;C:1298420335;G:1334893927;T:1262296331;N:57787	101	101	1302884238	1298420335	1334893927	1262296331	57787	SRX24301508	SRS21065427	SRA1848589	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.95719	0.95856	0.05756	0.05712	0.70534	0.70851	0.42046	0.41786	101	101	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Poland	2024-04-18	Larval	Larval	Eye	Sensory System
31850	31850	SRR28735528	SRX24301507	SRS21065426	SRP502615	PRJNA1101945	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [RNA seq]	GSE264309	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons. The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: AB and double knockout for stim2 stim2a;stim2b / zebrafish 5dpf larvae were used to isolate the total RNA from their eyes. The experimental setup involved 3 replicates per each condition stim2 KO vs control consisting of 35 eyes per repetition.	parent bioproject:PRJNA1101942	pubmed:39424970		stim2KO repllicate 2 RNASeq	GSM8215877		source name:eye\|tissue:eye\|genotype:stim2a;stim2b / \|age:5 dpf\|geo loc name:missing\|collection date:missing	stim2KO repllicate 2 RNASeq	Raw RNA seq data were converted to FASTQ format with bcl2fastq2 v2.17 Illumina and FastQC v0.11.4 was used to assess the quality of each sequencing run. We then utilized the SQuIRE pipeline45 for subsequent steps. STAR version 2.5.3a StringTie version 1.3.3b and DESeq2 version 1.16.149 were used within the SQuIRE pipeline for read alignment transcript assembly and quantification for each replicate and differential gene expression analysis respectively. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated files with raw reads for each sample	eye	Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer’s recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.	tissue:eye\|genotype:stim2a;stim2b / \|age:5 dpf	GSM8215877	GSM8215877: stim2KO repllicate 2 RNASeq; Danio rerio; RNA Seq	GSM8215877 r1	GSM8215877	1	Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer's recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP502615		loader:fastq load.py	mut_rep_2_R1_001.fastq.gz mut_rep_2_R2_001.fastq.gz	fastq fastq	5641008570.0	27925785.0	GSM8215877 r1	0:101 1:101	A:1421655053;C:1399106135;G:1439454285;T:1380731092;N:62005	101	101	1421655053	1399106135	1439454285	1380731092	62005	SRX24301507	SRS21065426	SRA1848589	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.95794	0.9601	0.05457	0.05365	0.70942	0.71151	0.42408	0.42666	101	101	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Poland	2024-04-18	Larval	Larval	Eye	Sensory System
31851	31851	SRR28735529	SRX24301506	SRS21065425	SRP502615	PRJNA1101945	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [RNA seq]	GSE264309	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons. The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: AB and double knockout for stim2 stim2a;stim2b / zebrafish 5dpf larvae were used to isolate the total RNA from their eyes. The experimental setup involved 3 replicates per each condition stim2 KO vs control consisting of 35 eyes per repetition.	parent bioproject:PRJNA1101942	pubmed:39424970		stim2KO repllicate 1 RNASeq	GSM8215876		source name:eye\|tissue:eye\|genotype:stim2a;stim2b / \|age:5 dpf\|geo loc name:missing\|collection date:missing	stim2KO repllicate 1 RNASeq	Raw RNA seq data were converted to FASTQ format with bcl2fastq2 v2.17 Illumina and FastQC v0.11.4 was used to assess the quality of each sequencing run. We then utilized the SQuIRE pipeline45 for subsequent steps. STAR version 2.5.3a StringTie version 1.3.3b and DESeq2 version 1.16.149 were used within the SQuIRE pipeline for read alignment transcript assembly and quantification for each replicate and differential gene expression analysis respectively. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated files with raw reads for each sample	eye	Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer’s recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.	tissue:eye\|genotype:stim2a;stim2b / \|age:5 dpf	GSM8215876	GSM8215876: stim2KO repllicate 1 RNASeq; Danio rerio; RNA Seq	GSM8215876 r1	GSM8215876	1	Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer's recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP502615		loader:fastq load.py	mut_rep_1_R1_001.fastq.gz mut_rep_1_R2_001.fastq.gz	fastq fastq	5147003026.0	25480213.0	GSM8215876 r1	0:101 1:101	A:1302966446;C:1274828722;G:1325578656;T:1243571921;N:57281	101	101	1302966446	1274828722	1325578656	1243571921	57281	SRX24301506	SRS21065425	SRA1848589	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.95963	0.96036	0.05042	0.05053	0.71275	0.71725	0.41458	0.41703	101	101	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Poland	2024-04-18	Larval	Larval	Eye	Sensory System
31852	31852	SRR28735530	SRX24301505	SRS21065424	SRP502615	PRJNA1101945	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [RNA seq]	GSE264309	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons. The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: AB and double knockout for stim2 stim2a;stim2b / zebrafish 5dpf larvae were used to isolate the total RNA from their eyes. The experimental setup involved 3 replicates per each condition stim2 KO vs control consisting of 35 eyes per repetition.	parent bioproject:PRJNA1101942	pubmed:39424970		Tg repllicate 3 RNASeq	GSM8215875		source name:eye\|tissue:eye\|genotype:AB\|age:5 dpf\|geo loc name:missing\|collection date:missing	Tg repllicate 3 RNASeq	Raw RNA seq data were converted to FASTQ format with bcl2fastq2 v2.17 Illumina and FastQC v0.11.4 was used to assess the quality of each sequencing run. We then utilized the SQuIRE pipeline45 for subsequent steps. STAR version 2.5.3a StringTie version 1.3.3b and DESeq2 version 1.16.149 were used within the SQuIRE pipeline for read alignment transcript assembly and quantification for each replicate and differential gene expression analysis respectively. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated files with raw reads for each sample	eye	Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer’s recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.	tissue:eye\|genotype:AB\|age:5 dpf	GSM8215875	GSM8215875: Tg repllicate 3 RNASeq; Danio rerio; RNA Seq	GSM8215875 r1	GSM8215875	1	Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer's recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP502615		loader:fastq load.py	wt_rep_3_R1_001.fastq.gz wt_rep_3_R2_001.fastq.gz	fastq fastq	4648345422.0	23011611.0	GSM8215875 r1	0:101 1:101	A:1186641846;C:1144216110;G:1192801277;T:1124633797;N:52392	101	101	1186641846	1144216110	1192801277	1124633797	52392	SRX24301505	SRS21065424	SRA1848589	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.9575	0.95756	0.05359	0.05311	0.69875	0.70315	0.42041	0.41054	101	101	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Poland	2024-04-18	Larval	Larval	Eye	Sensory System
31853	31853	SRR28735531	SRX24301504	SRS21065423	SRP502615	PRJNA1101945	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [RNA seq]	GSE264309	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons. The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: AB and double knockout for stim2 stim2a;stim2b / zebrafish 5dpf larvae were used to isolate the total RNA from their eyes. The experimental setup involved 3 replicates per each condition stim2 KO vs control consisting of 35 eyes per repetition.	parent bioproject:PRJNA1101942	pubmed:39424970		Tg repllicate 2 RNASeq	GSM8215874		source name:eye\|tissue:eye\|genotype:AB\|age:5 dpf\|geo loc name:missing\|collection date:missing	Tg repllicate 2 RNASeq	Raw RNA seq data were converted to FASTQ format with bcl2fastq2 v2.17 Illumina and FastQC v0.11.4 was used to assess the quality of each sequencing run. We then utilized the SQuIRE pipeline45 for subsequent steps. STAR version 2.5.3a StringTie version 1.3.3b and DESeq2 version 1.16.149 were used within the SQuIRE pipeline for read alignment transcript assembly and quantification for each replicate and differential gene expression analysis respectively. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated files with raw reads for each sample	eye	Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer’s recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.	tissue:eye\|genotype:AB\|age:5 dpf	GSM8215874	GSM8215874: Tg repllicate 2 RNASeq; Danio rerio; RNA Seq	GSM8215874 r1	GSM8215874	1	Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer's recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP502615		loader:fastq load.py	wt_rep_2_R1_001.fastq.gz wt_rep_2_R2_001.fastq.gz	fastq fastq	4769618546.0	23611973.0	GSM8215874 r1	0:101 1:101	A:1218890346;C:1171831021;G:1228410692;T:1150434539;N:51948	101	101	1218890346	1171831021	1228410692	1150434539	51948	SRX24301504	SRS21065423	SRA1848589	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.95682	0.95517	0.05192	0.05059	0.70849	0.71543	0.41181	0.41549	101	101	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Poland	2024-04-18	Larval	Larval	Eye	Sensory System
31854	31854	SRR28735532	SRX24301503	SRS21065422	SRP502615	PRJNA1101945	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [RNA seq]	GSE264309	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons. The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: AB and double knockout for stim2 stim2a;stim2b / zebrafish 5dpf larvae were used to isolate the total RNA from their eyes. The experimental setup involved 3 replicates per each condition stim2 KO vs control consisting of 35 eyes per repetition.	parent bioproject:PRJNA1101942	pubmed:39424970		Tg repllicate 1 RNASeq	GSM8215873		source name:eye\|tissue:eye\|genotype:AB\|age:5 dpf\|geo loc name:missing\|collection date:missing	Tg repllicate 1 RNASeq	Raw RNA seq data were converted to FASTQ format with bcl2fastq2 v2.17 Illumina and FastQC v0.11.4 was used to assess the quality of each sequencing run. We then utilized the SQuIRE pipeline45 for subsequent steps. STAR version 2.5.3a StringTie version 1.3.3b and DESeq2 version 1.16.149 were used within the SQuIRE pipeline for read alignment transcript assembly and quantification for each replicate and differential gene expression analysis respectively. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated files with raw reads for each sample	eye	Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer’s recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.	tissue:eye\|genotype:AB\|age:5 dpf	GSM8215873	GSM8215873: Tg repllicate 1 RNASeq; Danio rerio; RNA Seq	GSM8215873 r1	GSM8215873	1	Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer's recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP502615		loader:fastq load.py	wt_rep_1_R1_001.fastq.gz wt_rep_1_R2_001.fastq.gz	fastq fastq	4771981138.0	23623669.0	GSM8215873 r1	0:101 1:101	A:1222918015;C:1171619846;G:1231393968;T:1145997219;N:52090	101	101	1222918015	1171619846	1231393968	1145997219	52090	SRX24301503	SRS21065422	SRA1848589	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.95739	0.95621	0.05362	0.0539	0.71301	0.71979	0.42337	0.40836	101	101	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Poland	2024-04-18	Larval	Larval	Eye	Sensory System
32194	32194	SRR29141332	SRX24663085	SRS21398383	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Multiome rgc:ntr preablation wildtype control day 5 RNA	GSM8287442		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Multiome rgc:ntr preablation wildtype control day 5 RNA	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287442	GSM8287442: Multiome rgc:ntr preablation wildtype control day 5 RNA; Danio rerio; RNA Seq	GSM8287442 r1	GSM8287442	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH182R_S1_L001_R1_001.fastq.gz TH182R_S1_L001_R2_001.fastq.gz	fastq fastq	13807554173.0	116029867.0	GSM8287442 r1	0:28 1:91	A:4079582572;C:2862550576;G:2918085175;T:3947000701;N:335149	28	91	4079582572	2862550576	2918085175	3947000701	335149	SRX24663085	SRS21398383	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32195	32195	SRR29141333	SRX24663085	SRS21398383	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Multiome rgc:ntr preablation wildtype control day 5 RNA	GSM8287442		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Multiome rgc:ntr preablation wildtype control day 5 RNA	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287442	GSM8287442: Multiome rgc:ntr preablation wildtype control day 5 RNA; Danio rerio; RNA Seq	GSM8287442 r1	GSM8287442	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH182R_S1_L002_R1_001.fastq.gz TH182R_S1_L002_R2_001.fastq.gz	fastq fastq	13803126064.0	115992656.0	GSM8287442 r2	0:28 1:91	A:4078989982;C:2861718905;G:2916062814;T:3946005912;N:348451	28	91	4078989982	2861718905	2916062814	3946005912	348451	SRX24663085	SRS21398383	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32196	32196	SRR29141334	SRX24663085	SRS21398383	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Multiome rgc:ntr preablation wildtype control day 5 RNA	GSM8287442		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Multiome rgc:ntr preablation wildtype control day 5 RNA	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287442	GSM8287442: Multiome rgc:ntr preablation wildtype control day 5 RNA; Danio rerio; RNA Seq	GSM8287442 r1	GSM8287442	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH182R_S1_L003_R1_001.fastq.gz TH182R_S1_L003_R2_001.fastq.gz	fastq fastq	14039364150.0	117977850.0	GSM8287442 r3	0:28 1:91	A:4148421178;C:2910249087;G:2967774612;T:4012572976;N:346297	28	91	4148421178	2910249087	2967774612	4012572976	346297	SRX24663085	SRS21398383	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32197	32197	SRR29141335	SRX24663085	SRS21398383	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Multiome rgc:ntr preablation wildtype control day 5 RNA	GSM8287442		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Multiome rgc:ntr preablation wildtype control day 5 RNA	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287442	GSM8287442: Multiome rgc:ntr preablation wildtype control day 5 RNA; Danio rerio; RNA Seq	GSM8287442 r1	GSM8287442	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH182R_S1_L004_R1_001.fastq.gz TH182R_S1_L004_R2_001.fastq.gz	fastq fastq	14396508973.0	120979067.0	GSM8287442 r4	0:28 1:91	A:4252694309;C:2985039203;G:3045994377;T:4112440375;N:340709	28	91	4252694309	2985039203	3045994377	4112440375	340709	SRX24663085	SRS21398383	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32198	32198	SRR29141336	SRX24663084	SRS21398382	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 7 24h mtz	GSM8287437		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 7 24h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287437	GSM8287437: Ablated rgc:ntr day 7 24h mtz; Danio rerio; RNA Seq	GSM8287437 r1	GSM8287437	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH111_S65_R1_001.fastq.gz TH111_S65_R2_001.fastq.gz	fastq fastq	10009743191.0	84115489.0	GSM8287437 r1	0:28 1:91	A:2899067167;C:2137099335;G:2274433670;T:2671820531;N:27322488	28	91	2899067167	2137099335	2274433670	2671820531	27322488	SRX24663084	SRS21398382	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32199	32199	SRR29141337	SRX24663084	SRS21398382	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 7 24h mtz	GSM8287437		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 7 24h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287437	GSM8287437: Ablated rgc:ntr day 7 24h mtz; Danio rerio; RNA Seq	GSM8287437 r1	GSM8287437	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH111_S66_R1_001.fastq.gz TH111_S66_R2_001.fastq.gz	fastq fastq	10310944686.0	86646594.0	GSM8287437 r2	0:28 1:91	A:2991162064;C:2200127755;G:2335919653;T:2755298440;N:28436774	28	91	2991162064	2200127755	2335919653	2755298440	28436774	SRX24663084	SRS21398382	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32200	32200	SRR29141338	SRX24663084	SRS21398382	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 7 24h mtz	GSM8287437		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 7 24h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287437	GSM8287437: Ablated rgc:ntr day 7 24h mtz; Danio rerio; RNA Seq	GSM8287437 r1	GSM8287437	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH111_S68_R1_001.fastq.gz TH111_S68_R2_001.fastq.gz	fastq fastq	13987726480.0	117543920.0	GSM8287437 r3	0:28 1:91	A:4045259735;C:2989556292;G:3181238633;T:3733480210;N:38191610	28	91	4045259735	2989556292	3181238633	3733480210	38191610	SRX24663084	SRS21398382	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32201	32201	SRR29141339	SRX24663084	SRS21398382	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 7 24h mtz	GSM8287437		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 7 24h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287437	GSM8287437: Ablated rgc:ntr day 7 24h mtz; Danio rerio; RNA Seq	GSM8287437 r1	GSM8287437	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH111_S67_R1_001.fastq.gz TH111_S67_R2_001.fastq.gz	fastq fastq	11876682069.0	99804051.0	GSM8287437 r4	0:28 1:91	A:3432787756;C:2538691346;G:2701757248;T:3170892876;N:32552843	28	91	3432787756	2538691346	2701757248	3170892876	32552843	SRX24663084	SRS21398382	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32202	32202	SRR29141340	SRX24663083	SRS21398381	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 9 72h mtz	GSM8287441		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 9 72h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287441	GSM8287441: Ablated rgc:ntr day 9 72h mtz; Danio rerio; RNA Seq	GSM8287441 r1	GSM8287441	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH136_S61_L001_R1_001.fastq.gz TH136_S61_L001_R2_001.fastq.gz	fastq fastq	4774895706.0	40125174.0	GSM8287441 r1	0:28 1:91	A:1351265716;C:1042777184;G:1100567875;T:1280161557;N:123374	28	91	1351265716	1042777184	1100567875	1280161557	123374	SRX24663083	SRS21398381	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32203	32203	SRR29141341	SRX24663083	SRS21398381	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 9 72h mtz	GSM8287441		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 9 72h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287441	GSM8287441: Ablated rgc:ntr day 9 72h mtz; Danio rerio; RNA Seq	GSM8287441 r1	GSM8287441	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH136_S64_L003_R1_001.fastq.gz TH136_S64_L003_R2_001.fastq.gz	fastq fastq	5538657579.0	46543341.0	GSM8287441 r10	0:28 1:91	A:1567217187;C:1211616483;G:1275241958;T:1484449584;N:132367	28	91	1567217187	1211616483	1275241958	1484449584	132367	SRX24663083	SRS21398381	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32204	32204	SRR29141342	SRX24663083	SRS21398381	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 9 72h mtz	GSM8287441		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 9 72h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287441	GSM8287441: Ablated rgc:ntr day 9 72h mtz; Danio rerio; RNA Seq	GSM8287441 r1	GSM8287441	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH136_S64_L004_R1_001.fastq.gz TH136_S64_L004_R2_001.fastq.gz	fastq fastq	5403469057.0	45407303.0	GSM8287441 r11	0:28 1:91	A:1530355512;C:1180686287;G:1242924943;T:1449389493;N:112822	28	91	1530355512	1180686287	1242924943	1449389493	112822	SRX24663083	SRS21398381	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32205	32205	SRR29141343	SRX24663083	SRS21398381	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 9 72h mtz	GSM8287441		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 9 72h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287441	GSM8287441: Ablated rgc:ntr day 9 72h mtz; Danio rerio; RNA Seq	GSM8287441 r1	GSM8287441	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH136_S61_L002_R1_001.fastq.gz TH136_S61_L002_R2_001.fastq.gz	fastq fastq	4786338627.0	40221333.0	GSM8287441 r12	0:28 1:91	A:1355122219;C:1044516973;G:1101760300;T:1284824360;N:114775	28	91	1355122219	1044516973	1101760300	1284824360	114775	SRX24663083	SRS21398381	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32206	32206	SRR29141344	SRX24663083	SRS21398381	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 9 72h mtz	GSM8287441		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 9 72h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287441	GSM8287441: Ablated rgc:ntr day 9 72h mtz; Danio rerio; RNA Seq	GSM8287441 r1	GSM8287441	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH136_S62_L001_R1_001.fastq.gz TH136_S62_L001_R2_001.fastq.gz	fastq fastq	4901760535.0	41191265.0	GSM8287441 r13	0:28 1:91	A:1391714409;C:1068852387;G:1124767182;T:1316299153;N:127404	28	91	1391714409	1068852387	1124767182	1316299153	127404	SRX24663083	SRS21398381	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32207	32207	SRR29141345	SRX24663083	SRS21398381	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 9 72h mtz	GSM8287441		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 9 72h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287441	GSM8287441: Ablated rgc:ntr day 9 72h mtz; Danio rerio; RNA Seq	GSM8287441 r1	GSM8287441	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH136_S62_L004_R1_001.fastq.gz TH136_S62_L004_R2_001.fastq.gz	fastq fastq	4937865968.0	41494672.0	GSM8287441 r14	0:28 1:91	A:1399404530;C:1078622301;G:1134489765;T:1325245845;N:103527	28	91	1399404530	1078622301	1134489765	1325245845	103527	SRX24663083	SRS21398381	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32208	32208	SRR29141346	SRX24663083	SRS21398381	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 9 72h mtz	GSM8287441		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 9 72h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287441	GSM8287441: Ablated rgc:ntr day 9 72h mtz; Danio rerio; RNA Seq	GSM8287441 r1	GSM8287441	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH136_S63_L003_R1_001.fastq.gz TH136_S63_L003_R2_001.fastq.gz	fastq fastq	4497873940.0	37797260.0	GSM8287441 r15	0:28 1:91	A:1271859460;C:985043807;G:1034974096;T:1205889617;N:106960	28	91	1271859460	985043807	1034974096	1205889617	106960	SRX24663083	SRS21398381	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32209	32209	SRR29141347	SRX24663083	SRS21398381	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 9 72h mtz	GSM8287441		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 9 72h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287441	GSM8287441: Ablated rgc:ntr day 9 72h mtz; Danio rerio; RNA Seq	GSM8287441 r1	GSM8287441	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH136_S64_L002_R1_001.fastq.gz TH136_S64_L002_R2_001.fastq.gz	fastq fastq	5236234787.0	44001973.0	GSM8287441 r16	0:28 1:91	A:1486231119;C:1141729846;G:1201608482;T:1406539690;N:125650	28	91	1486231119	1141729846	1201608482	1406539690	125650	SRX24663083	SRS21398381	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32210	32210	SRR29141348	SRX24663083	SRS21398381	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 9 72h mtz	GSM8287441		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 9 72h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287441	GSM8287441: Ablated rgc:ntr day 9 72h mtz; Danio rerio; RNA Seq	GSM8287441 r1	GSM8287441	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH136_S61_L003_R1_001.fastq.gz TH136_S61_L003_R2_001.fastq.gz	fastq fastq	5047989877.0	42420083.0	GSM8287441 r2	0:28 1:91	A:1424658452;C:1105197562;G:1165585488;T:1352428003;N:120372	28	91	1424658452	1105197562	1165585488	1352428003	120372	SRX24663083	SRS21398381	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32211	32211	SRR29141349	SRX24663083	SRS21398381	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 9 72h mtz	GSM8287441		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 9 72h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287441	GSM8287441: Ablated rgc:ntr day 9 72h mtz; Danio rerio; RNA Seq	GSM8287441 r1	GSM8287441	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH136_S61_L004_R1_001.fastq.gz TH136_S61_L004_R2_001.fastq.gz	fastq fastq	4922634682.0	41366678.0	GSM8287441 r3	0:28 1:91	A:1390880945;C:1076385249;G:1135254796;T:1320011695;N:101997	28	91	1390880945	1076385249	1135254796	1320011695	101997	SRX24663083	SRS21398381	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32212	32212	SRR29141350	SRX24663083	SRS21398381	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 9 72h mtz	GSM8287441		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 9 72h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287441	GSM8287441: Ablated rgc:ntr day 9 72h mtz; Danio rerio; RNA Seq	GSM8287441 r1	GSM8287441	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH136_S62_L002_R1_001.fastq.gz TH136_S62_L002_R2_001.fastq.gz	fastq fastq	4903434746.0	41205334.0	GSM8287441 r4	0:28 1:91	A:1392700449;C:1068492247;G:1123677701;T:1318447188;N:117161	28	91	1392700449	1068492247	1123677701	1318447188	117161	SRX24663083	SRS21398381	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32213	32213	SRR29141351	SRX24663083	SRS21398381	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 9 72h mtz	GSM8287441		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 9 72h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287441	GSM8287441: Ablated rgc:ntr day 9 72h mtz; Danio rerio; RNA Seq	GSM8287441 r1	GSM8287441	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH136_S62_L003_R1_001.fastq.gz TH136_S62_L003_R2_001.fastq.gz	fastq fastq	5079175136.0	42682144.0	GSM8287441 r5	0:28 1:91	A:1438032514;C:1110731492;G:1168141629;T:1362147196;N:122305	28	91	1438032514	1110731492	1168141629	1362147196	122305	SRX24663083	SRS21398381	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32214	32214	SRR29141352	SRX24663083	SRS21398381	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 9 72h mtz	GSM8287441		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 9 72h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287441	GSM8287441: Ablated rgc:ntr day 9 72h mtz; Danio rerio; RNA Seq	GSM8287441 r1	GSM8287441	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH136_S63_L001_R1_001.fastq.gz TH136_S63_L001_R2_001.fastq.gz	fastq fastq	4248222293.0	35699347.0	GSM8287441 r6	0:28 1:91	A:1204282194;C:928219300;G:975617558;T:1139994829;N:108412	28	91	1204282194	928219300	975617558	1139994829	108412	SRX24663083	SRS21398381	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32215	32215	SRR29141353	SRX24663083	SRS21398381	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 9 72h mtz	GSM8287441		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 9 72h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287441	GSM8287441: Ablated rgc:ntr day 9 72h mtz; Danio rerio; RNA Seq	GSM8287441 r1	GSM8287441	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH136_S63_L002_R1_001.fastq.gz TH136_S63_L002_R2_001.fastq.gz	fastq fastq	4256614411.0	35769869.0	GSM8287441 r7	0:28 1:91	A:1207165748;C:929375627;G:976155057;T:1143817351;N:100628	28	91	1207165748	929375627	976155057	1143817351	100628	SRX24663083	SRS21398381	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32216	32216	SRR29141354	SRX24663083	SRS21398381	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 9 72h mtz	GSM8287441		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 9 72h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287441	GSM8287441: Ablated rgc:ntr day 9 72h mtz; Danio rerio; RNA Seq	GSM8287441 r1	GSM8287441	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH136_S63_L004_R1_001.fastq.gz TH136_S63_L004_R2_001.fastq.gz	fastq fastq	4376437534.0	36776786.0	GSM8287441 r8	0:28 1:91	A:1238798346;C:957263182;G:1005958070;T:1174327377;N:90559	28	91	1238798346	957263182	1005958070	1174327377	90559	SRX24663083	SRS21398381	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32217	32217	SRR29141355	SRX24663083	SRS21398381	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 9 72h mtz	GSM8287441		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 9 72h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287441	GSM8287441: Ablated rgc:ntr day 9 72h mtz; Danio rerio; RNA Seq	GSM8287441 r1	GSM8287441	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH136_S64_L001_R1_001.fastq.gz TH136_S64_L001_R2_001.fastq.gz	fastq fastq	5222497546.0	43886534.0	GSM8287441 r9	0:28 1:91	A:1481856778;C:1139695420;G:1200133908;T:1400676121;N:135319	28	91	1481856778	1139695420	1200133908	1400676121	135319	SRX24663083	SRS21398381	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32218	32218	SRR29141356	SRX24663082	SRS21398380	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 6 12h mtz	GSM8287440		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 6 12h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287440	GSM8287440: Ablated rgc:ntr day 6 12h mtz; Danio rerio; RNA Seq	GSM8287440 r1	GSM8287440	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH135_S57_L001_R1_001.fastq.gz TH135_S57_L001_R2_001.fastq.gz	fastq fastq	4775761788.0	40132452.0	GSM8287440 r1	0:28 1:91	A:1364997508;C:1030536901;G:1087120578;T:1292982564;N:124237	28	91	1364997508	1030536901	1087120578	1292982564	124237	SRX24663082	SRS21398380	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32219	32219	SRR29141357	SRX24663082	SRS21398380	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 6 12h mtz	GSM8287440		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 6 12h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287440	GSM8287440: Ablated rgc:ntr day 6 12h mtz; Danio rerio; RNA Seq	GSM8287440 r1	GSM8287440	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH135_S60_L002_R1_001.fastq.gz TH135_S60_L002_R2_001.fastq.gz	fastq fastq	5081243356.0	42699524.0	GSM8287440 r10	0:28 1:91	A:1453763884;C:1095418883;G:1154387721;T:1377550690;N:122178	28	91	1453763884	1095418883	1154387721	1377550690	122178	SRX24663082	SRS21398380	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32220	32220	SRR29141358	SRX24663082	SRS21398380	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 6 12h mtz	GSM8287440		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 6 12h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287440	GSM8287440: Ablated rgc:ntr day 6 12h mtz; Danio rerio; RNA Seq	GSM8287440 r1	GSM8287440	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH135_S60_L004_R1_001.fastq.gz TH135_S60_L004_R2_001.fastq.gz	fastq fastq	5258119482.0	44185878.0	GSM8287440 r11	0:28 1:91	A:1501504527;C:1135881534;G:1197368112;T:1423254847;N:110462	28	91	1501504527	1135881534	1197368112	1423254847	110462	SRX24663082	SRS21398380	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32221	32221	SRR29141359	SRX24663082	SRS21398380	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 6 12h mtz	GSM8287440		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 6 12h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287440	GSM8287440: Ablated rgc:ntr day 6 12h mtz; Danio rerio; RNA Seq	GSM8287440 r1	GSM8287440	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH135_S57_L003_R1_001.fastq.gz TH135_S57_L003_R2_001.fastq.gz	fastq fastq	5008964184.0	42092136.0	GSM8287440 r12	0:28 1:91	A:1428212274;C:1083563490;G:1142704874;T:1354362571;N:120975	28	91	1428212274	1083563490	1142704874	1354362571	120975	SRX24663082	SRS21398380	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32222	32222	SRR29141360	SRX24663082	SRS21398380	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 6 12h mtz	GSM8287440		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 6 12h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287440	GSM8287440: Ablated rgc:ntr day 6 12h mtz; Danio rerio; RNA Seq	GSM8287440 r1	GSM8287440	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH135_S58_L002_R1_001.fastq.gz TH135_S58_L002_R2_001.fastq.gz	fastq fastq	5035503207.0	42315153.0	GSM8287440 r13	0:28 1:91	A:1440077950;C:1086334843;G:1144377517;T:1364592460;N:120437	28	91	1440077950	1086334843	1144377517	1364592460	120437	SRX24663082	SRS21398380	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32223	32223	SRR29141361	SRX24663082	SRS21398380	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 6 12h mtz	GSM8287440		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 6 12h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287440	GSM8287440: Ablated rgc:ntr day 6 12h mtz; Danio rerio; RNA Seq	GSM8287440 r1	GSM8287440	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH135_S59_L001_R1_001.fastq.gz TH135_S59_L001_R2_001.fastq.gz	fastq fastq	5387099536.0	45269744.0	GSM8287440 r14	0:28 1:91	A:1537849058;C:1163912984;G:1227124886;T:1458073621;N:138987	28	91	1537849058	1163912984	1227124886	1458073621	138987	SRX24663082	SRS21398380	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32224	32224	SRR29141362	SRX24663082	SRS21398380	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 6 12h mtz	GSM8287440		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 6 12h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287440	GSM8287440: Ablated rgc:ntr day 6 12h mtz; Danio rerio; RNA Seq	GSM8287440 r1	GSM8287440	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH135_S59_L004_R1_001.fastq.gz TH135_S59_L004_R2_001.fastq.gz	fastq fastq	5512521490.0	46323710.0	GSM8287440 r15	0:28 1:91	A:1571984524;C:1192238932;G:1256792838;T:1491389888;N:115308	28	91	1571984524	1192238932	1256792838	1491389888	115308	SRX24663082	SRS21398380	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32225	32225	SRR29141363	SRX24663082	SRS21398380	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 6 12h mtz	GSM8287440		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 6 12h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287440	GSM8287440: Ablated rgc:ntr day 6 12h mtz; Danio rerio; RNA Seq	GSM8287440 r1	GSM8287440	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH135_S60_L003_R1_001.fastq.gz TH135_S60_L003_R2_001.fastq.gz	fastq fastq	5376169386.0	45177894.0	GSM8287440 r16	0:28 1:91	A:1533658425;C:1162739111;G:1225658907;T:1453983443;N:129500	28	91	1533658425	1162739111	1225658907	1453983443	129500	SRX24663082	SRS21398380	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32226	32226	SRR29141364	SRX24663082	SRS21398380	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 6 12h mtz	GSM8287440		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 6 12h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287440	GSM8287440: Ablated rgc:ntr day 6 12h mtz; Danio rerio; RNA Seq	GSM8287440 r1	GSM8287440	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH135_S57_L002_R1_001.fastq.gz TH135_S57_L002_R2_001.fastq.gz	fastq fastq	4787380115.0	40230085.0	GSM8287440 r2	0:28 1:91	A:1368967190;C:1032261634;G:1088378612;T:1297658513;N:114166	28	91	1368967190	1032261634	1088378612	1297658513	114166	SRX24663082	SRS21398380	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32227	32227	SRR29141365	SRX24663082	SRS21398380	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 6 12h mtz	GSM8287440		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 6 12h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287440	GSM8287440: Ablated rgc:ntr day 6 12h mtz; Danio rerio; RNA Seq	GSM8287440 r1	GSM8287440	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH135_S57_L004_R1_001.fastq.gz TH135_S57_L004_R2_001.fastq.gz	fastq fastq	4885123145.0	41051455.0	GSM8287440 r3	0:28 1:91	A:1394450278;C:1055564129;G:1113114189;T:1321891090;N:103459	28	91	1394450278	1055564129	1113114189	1321891090	103459	SRX24663082	SRS21398380	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32228	32228	SRR29141366	SRX24663082	SRS21398380	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 6 12h mtz	GSM8287440		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 6 12h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287440	GSM8287440: Ablated rgc:ntr day 6 12h mtz; Danio rerio; RNA Seq	GSM8287440 r1	GSM8287440	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH135_S58_L001_R1_001.fastq.gz TH135_S58_L001_R2_001.fastq.gz	fastq fastq	5060757982.0	42527378.0	GSM8287440 r4	0:28 1:91	A:1446313544;C:1092878434;G:1151738503;T:1369695242;N:132259	28	91	1446313544	1092878434	1151738503	1369695242	132259	SRX24663082	SRS21398380	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32229	32229	SRR29141367	SRX24663082	SRS21398380	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 6 12h mtz	GSM8287440		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 6 12h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287440	GSM8287440: Ablated rgc:ntr day 6 12h mtz; Danio rerio; RNA Seq	GSM8287440 r1	GSM8287440	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH135_S58_L003_R1_001.fastq.gz TH135_S58_L003_R2_001.fastq.gz	fastq fastq	5322898560.0	44730240.0	GSM8287440 r5	0:28 1:91	A:1517934750;C:1151967941;G:1213786668;T:1439081677;N:127524	28	91	1517934750	1151967941	1213786668	1439081677	127524	SRX24663082	SRS21398380	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32230	32230	SRR29141368	SRX24663082	SRS21398380	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 6 12h mtz	GSM8287440		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 6 12h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287440	GSM8287440: Ablated rgc:ntr day 6 12h mtz; Danio rerio; RNA Seq	GSM8287440 r1	GSM8287440	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH135_S58_L004_R1_001.fastq.gz TH135_S58_L004_R2_001.fastq.gz	fastq fastq	5160850786.0	43368494.0	GSM8287440 r6	0:28 1:91	A:1473328102;C:1115516878;G:1175502159;T:1396395641;N:108006	28	91	1473328102	1115516878	1175502159	1396395641	108006	SRX24663082	SRS21398380	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32231	32231	SRR29141369	SRX24663082	SRS21398380	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 6 12h mtz	GSM8287440		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 6 12h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287440	GSM8287440: Ablated rgc:ntr day 6 12h mtz; Danio rerio; RNA Seq	GSM8287440 r1	GSM8287440	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH135_S59_L002_R1_001.fastq.gz TH135_S59_L002_R2_001.fastq.gz	fastq fastq	5381504513.0	45222727.0	GSM8287440 r7	0:28 1:91	A:1537238062;C:1161721381;G:1224135102;T:1458280892;N:129076	28	91	1537238062	1161721381	1224135102	1458280892	129076	SRX24663082	SRS21398380	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32232	32232	SRR29141370	SRX24663082	SRS21398380	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 6 12h mtz	GSM8287440		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 6 12h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287440	GSM8287440: Ablated rgc:ntr day 6 12h mtz; Danio rerio; RNA Seq	GSM8287440 r1	GSM8287440	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH135_S59_L003_R1_001.fastq.gz TH135_S59_L003_R2_001.fastq.gz	fastq fastq	5665367827.0	47608133.0	GSM8287440 r8	0:28 1:91	A:1613897652;C:1226812698;G:1293000098;T:1531521187;N:136192	28	91	1613897652	1226812698	1293000098	1531521187	136192	SRX24663082	SRS21398380	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32233	32233	SRR29141371	SRX24663082	SRS21398380	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Ablated rgc:ntr day 6 12h mtz	GSM8287440		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz\|geo loc name:missing\|collection date:missing	Ablated rgc:ntr day 6 12h mtz	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:mtz	GSM8287440	GSM8287440: Ablated rgc:ntr day 6 12h mtz; Danio rerio; RNA Seq	GSM8287440 r1	GSM8287440	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH135_S60_L001_R1_001.fastq.gz TH135_S60_L001_R2_001.fastq.gz	fastq fastq	5045550377.0	42399583.0	GSM8287440 r9	0:28 1:91	A:1442885146;C:1088672739;G:1147630180;T:1366230521;N:131791	28	91	1442885146	1088672739	1147630180	1366230521	131791	SRX24663082	SRS21398380	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32234	32234	SRR29141372	SRX24663081	SRS21398379	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 9	GSM8287439		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 9	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287439	GSM8287439: Unablated rgc:ntr day 9; Danio rerio; RNA Seq	GSM8287439 r1	GSM8287439	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH134_S53_L001_R1_001.fastq.gz TH134_S53_L001_R2_001.fastq.gz	fastq fastq	4566870378.0	38377062.0	GSM8287439 r1	0:28 1:91	A:1300193484;C:990777876;G:1047244494;T:1228536400;N:118124	28	91	1300193484	990777876	1047244494	1228536400	118124	SRX24663081	SRS21398379	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32235	32235	SRR29141373	SRX24663081	SRS21398379	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 9	GSM8287439		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 9	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287439	GSM8287439: Unablated rgc:ntr day 9; Danio rerio; RNA Seq	GSM8287439 r1	GSM8287439	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH134_S55_L002_R1_001.fastq.gz TH134_S55_L002_R2_001.fastq.gz	fastq fastq	4872575309.0	40946011.0	GSM8287439 r10	0:28 1:91	A:1388373514;C:1056698672;G:1113330484;T:1314056163;N:116476	28	91	1388373514	1056698672	1113330484	1314056163	116476	SRX24663081	SRS21398379	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32236	32236	SRR29141374	SRX24663081	SRS21398379	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 9	GSM8287439		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 9	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287439	GSM8287439: Unablated rgc:ntr day 9; Danio rerio; RNA Seq	GSM8287439 r1	GSM8287439	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH134_S55_L003_R1_001.fastq.gz TH134_S55_L003_R2_001.fastq.gz	fastq fastq	5138052528.0	43176912.0	GSM8287439 r11	0:28 1:91	A:1459926271;C:1117597394;G:1177808023;T:1382597761;N:123079	28	91	1459926271	1117597394	1177808023	1382597761	123079	SRX24663081	SRS21398379	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32237	32237	SRR29141375	SRX24663081	SRS21398379	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 9	GSM8287439		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 9	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287439	GSM8287439: Unablated rgc:ntr day 9; Danio rerio; RNA Seq	GSM8287439 r1	GSM8287439	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH134_S55_L004_R1_001.fastq.gz TH134_S55_L004_R2_001.fastq.gz	fastq fastq	5022868263.0	42208977.0	GSM8287439 r12	0:28 1:91	A:1428914798;C:1091192534;G:1150147876;T:1352508063;N:104992	28	91	1428914798	1091192534	1150147876	1352508063	104992	SRX24663081	SRS21398379	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32238	32238	SRR29141376	SRX24663081	SRS21398379	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 9	GSM8287439		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 9	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287439	GSM8287439: Unablated rgc:ntr day 9; Danio rerio; RNA Seq	GSM8287439 r1	GSM8287439	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH134_S56_L001_R1_001.fastq.gz TH134_S56_L001_R2_001.fastq.gz	fastq fastq	4569776953.0	38401487.0	GSM8287439 r13	0:28 1:91	A:1299842950;C:992232187;G:1048131188;T:1229452715;N:117913	28	91	1299842950	992232187	1048131188	1229452715	117913	SRX24663081	SRS21398379	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32239	32239	SRR29141377	SRX24663081	SRS21398379	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 9	GSM8287439		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 9	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287439	GSM8287439: Unablated rgc:ntr day 9; Danio rerio; RNA Seq	GSM8287439 r1	GSM8287439	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH134_S56_L002_R1_001.fastq.gz TH134_S56_L002_R2_001.fastq.gz	fastq fastq	4604427135.0	38692665.0	GSM8287439 r14	0:28 1:91	A:1310481305;C:998823194;G:1054488359;T:1240523819;N:110458	28	91	1310481305	998823194	1054488359	1240523819	110458	SRX24663081	SRS21398379	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32240	32240	SRR29141378	SRX24663081	SRS21398379	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 9	GSM8287439		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 9	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287439	GSM8287439: Unablated rgc:ntr day 9; Danio rerio; RNA Seq	GSM8287439 r1	GSM8287439	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH134_S56_L003_R1_001.fastq.gz TH134_S56_L003_R2_001.fastq.gz	fastq fastq	4894210580.0	41127820.0	GSM8287439 r15	0:28 1:91	A:1389263901;C:1064650503;G:1124176385;T:1316003245;N:116546	28	91	1389263901	1064650503	1124176385	1316003245	116546	SRX24663081	SRS21398379	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32241	32241	SRR29141379	SRX24663081	SRS21398379	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 9	GSM8287439		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 9	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287439	GSM8287439: Unablated rgc:ntr day 9; Danio rerio; RNA Seq	GSM8287439 r1	GSM8287439	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH134_S56_L004_R1_001.fastq.gz TH134_S56_L004_R2_001.fastq.gz	fastq fastq	4782327494.0	40187626.0	GSM8287439 r16	0:28 1:91	A:1359054303;C:1039048484;G:1097178265;T:1286945985;N:100457	28	91	1359054303	1039048484	1097178265	1286945985	100457	SRX24663081	SRS21398379	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32242	32242	SRR29141380	SRX24663081	SRS21398379	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 9	GSM8287439		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 9	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287439	GSM8287439: Unablated rgc:ntr day 9; Danio rerio; RNA Seq	GSM8287439 r1	GSM8287439	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH134_S53_L002_R1_001.fastq.gz TH134_S53_L002_R2_001.fastq.gz	fastq fastq	4587896012.0	38553748.0	GSM8287439 r2	0:28 1:91	A:1307093057;C:994483546;G:1050434019;T:1235776211;N:109179	28	91	1307093057	994483546	1050434019	1235776211	109179	SRX24663081	SRS21398379	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32243	32243	SRR29141381	SRX24663081	SRS21398379	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 9	GSM8287439		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 9	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287439	GSM8287439: Unablated rgc:ntr day 9; Danio rerio; RNA Seq	GSM8287439 r1	GSM8287439	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH134_S53_L003_R1_001.fastq.gz TH134_S53_L003_R2_001.fastq.gz	fastq fastq	4853618728.0	40786712.0	GSM8287439 r3	0:28 1:91	A:1378590543;C:1055361040;G:1114790969;T:1304760000;N:116176	28	91	1378590543	1055361040	1114790969	1304760000	116176	SRX24663081	SRS21398379	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32244	32244	SRR29141382	SRX24663081	SRS21398379	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 9	GSM8287439		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 9	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287439	GSM8287439: Unablated rgc:ntr day 9; Danio rerio; RNA Seq	GSM8287439 r1	GSM8287439	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH134_S53_L004_R1_001.fastq.gz TH134_S53_L004_R2_001.fastq.gz	fastq fastq	4736870803.0	39805637.0	GSM8287439 r4	0:28 1:91	A:1346988869;C:1028744736;G:1086568704;T:1274469646;N:98848	28	91	1346988869	1028744736	1086568704	1274469646	98848	SRX24663081	SRS21398379	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32245	32245	SRR29141383	SRX24663081	SRS21398379	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 9	GSM8287439		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 9	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287439	GSM8287439: Unablated rgc:ntr day 9; Danio rerio; RNA Seq	GSM8287439 r1	GSM8287439	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH134_S54_L001_R1_001.fastq.gz TH134_S54_L001_R2_001.fastq.gz	fastq fastq	5319795040.0	44704160.0	GSM8287439 r5	0:28 1:91	A:1516665110;C:1153199308;G:1216078023;T:1433713315;N:139284	28	91	1516665110	1153199308	1216078023	1433713315	139284	SRX24663081	SRS21398379	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32246	32246	SRR29141384	SRX24663081	SRS21398379	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 9	GSM8287439		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 9	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287439	GSM8287439: Unablated rgc:ntr day 9; Danio rerio; RNA Seq	GSM8287439 r1	GSM8287439	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH134_S54_L002_R1_001.fastq.gz TH134_S54_L002_R2_001.fastq.gz	fastq fastq	5330566682.0	44794678.0	GSM8287439 r6	0:28 1:91	A:1520480633;C:1154635844;G:1217037822;T:1438283496;N:128887	28	91	1520480633	1154635844	1217037822	1438283496	128887	SRX24663081	SRS21398379	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32247	32247	SRR29141385	SRX24663081	SRS21398379	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 9	GSM8287439		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 9	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287439	GSM8287439: Unablated rgc:ntr day 9; Danio rerio; RNA Seq	GSM8287439 r1	GSM8287439	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH134_S54_L003_R1_001.fastq.gz TH134_S54_L003_R2_001.fastq.gz	fastq fastq	5561785705.0	46737695.0	GSM8287439 r7	0:28 1:91	A:1581477655;C:1208929874;G:1274395111;T:1496847765;N:135300	28	91	1581477655	1208929874	1274395111	1496847765	135300	SRX24663081	SRS21398379	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32248	32248	SRR29141386	SRX24663081	SRS21398379	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 9	GSM8287439		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 9	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287439	GSM8287439: Unablated rgc:ntr day 9; Danio rerio; RNA Seq	GSM8287439 r1	GSM8287439	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH134_S54_L004_R1_001.fastq.gz TH134_S54_L004_R2_001.fastq.gz	fastq fastq	5423072403.0	45572037.0	GSM8287439 r8	0:28 1:91	A:1543580201;C:1177607853;G:1241277315;T:1460492382;N:114652	28	91	1543580201	1177607853	1241277315	1460492382	114652	SRX24663081	SRS21398379	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32249	32249	SRR29141387	SRX24663081	SRS21398379	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 9	GSM8287439		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 9	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287439	GSM8287439: Unablated rgc:ntr day 9; Danio rerio; RNA Seq	GSM8287439 r1	GSM8287439	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH134_S55_L001_R1_001.fastq.gz TH134_S55_L001_R2_001.fastq.gz	fastq fastq	4848214105.0	40741295.0	GSM8287439 r9	0:28 1:91	A:1380197121;C:1052472596;G:1109522284;T:1305896718;N:125386	28	91	1380197121	1052472596	1109522284	1305896718	125386	SRX24663081	SRS21398379	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32250	32250	SRR29141388	SRX24663080	SRS21398378	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 6	GSM8287438		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 6	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287438	GSM8287438: Unablated rgc:ntr day 6; Danio rerio; RNA Seq	GSM8287438 r1	GSM8287438	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH133_S49_L001_R1_001.fastq.gz TH133_S49_L001_R2_001.fastq.gz	fastq fastq	4633962102.0	38940858.0	GSM8287438 r1	0:28 1:91	A:1297725412;C:1024809339;G:1076904995;T:1234401645;N:120711	28	91	1297725412	1024809339	1076904995	1234401645	120711	SRX24663080	SRS21398378	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32251	32251	SRR29141389	SRX24663080	SRS21398378	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 6	GSM8287438		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 6	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287438	GSM8287438: Unablated rgc:ntr day 6; Danio rerio; RNA Seq	GSM8287438 r1	GSM8287438	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH133_S52_L003_R1_001.fastq.gz TH133_S52_L003_R2_001.fastq.gz	fastq fastq	4989425217.0	41927943.0	GSM8287438 r10	0:28 1:91	A:1391245093;C:1106917719;G:1165216341;T:1325928222;N:117842	28	91	1391245093	1106917719	1165216341	1325928222	117842	SRX24663080	SRS21398378	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32252	32252	SRR29141390	SRX24663080	SRS21398378	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 6	GSM8287438		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 6	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287438	GSM8287438: Unablated rgc:ntr day 6; Danio rerio; RNA Seq	GSM8287438 r1	GSM8287438	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH133_S52_L004_R1_001.fastq.gz TH133_S52_L004_R2_001.fastq.gz	fastq fastq	4854872155.0	40797245.0	GSM8287438 r11	0:28 1:91	A:1355524409;C:1075673845;G:1132295861;T:1291276543;N:101497	28	91	1355524409	1075673845	1132295861	1291276543	101497	SRX24663080	SRS21398378	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32253	32253	SRR29141391	SRX24663080	SRS21398378	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 6	GSM8287438		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 6	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287438	GSM8287438: Unablated rgc:ntr day 6; Danio rerio; RNA Seq	GSM8287438 r1	GSM8287438	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH133_S49_L002_R1_001.fastq.gz TH133_S49_L002_R2_001.fastq.gz	fastq fastq	4657232314.0	39136406.0	GSM8287438 r12	0:28 1:91	A:1305512663;C:1028718382;G:1080733287;T:1242157091;N:110891	28	91	1305512663	1028718382	1080733287	1242157091	110891	SRX24663080	SRS21398378	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32254	32254	SRR29141392	SRX24663080	SRS21398378	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 6	GSM8287438		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 6	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287438	GSM8287438: Unablated rgc:ntr day 6; Danio rerio; RNA Seq	GSM8287438 r1	GSM8287438	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH133_S50_L001_R1_001.fastq.gz TH133_S50_L001_R2_001.fastq.gz	fastq fastq	4932588794.0	41450326.0	GSM8287438 r13	0:28 1:91	A:1379015030;C:1091338503;G:1149356127;T:1312752653;N:126481	28	91	1379015030	1091338503	1149356127	1312752653	126481	SRX24663080	SRS21398378	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32255	32255	SRR29141393	SRX24663080	SRS21398378	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 6	GSM8287438		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 6	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287438	GSM8287438: Unablated rgc:ntr day 6; Danio rerio; RNA Seq	GSM8287438 r1	GSM8287438	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH133_S50_L004_R1_001.fastq.gz TH133_S50_L004_R2_001.fastq.gz	fastq fastq	5077097277.0	42664683.0	GSM8287438 r14	0:28 1:91	A:1418123656;C:1124378298;G:1183528228;T:1350962964;N:104131	28	91	1418123656	1124378298	1183528228	1350962964	104131	SRX24663080	SRS21398378	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32256	32256	SRR29141394	SRX24663080	SRS21398378	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 6	GSM8287438		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 6	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287438	GSM8287438: Unablated rgc:ntr day 6; Danio rerio; RNA Seq	GSM8287438 r1	GSM8287438	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH133_S51_L003_R1_001.fastq.gz TH133_S51_L003_R2_001.fastq.gz	fastq fastq	4923689498.0	41375542.0	GSM8287438 r15	0:28 1:91	A:1375204406;C:1090796811;G:1149080188;T:1308491701;N:116392	28	91	1375204406	1090796811	1149080188	1308491701	116392	SRX24663080	SRS21398378	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32257	32257	SRR29141395	SRX24663080	SRS21398378	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 6	GSM8287438		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 6	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287438	GSM8287438: Unablated rgc:ntr day 6; Danio rerio; RNA Seq	GSM8287438 r1	GSM8287438	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH133_S52_L002_R1_001.fastq.gz TH133_S52_L002_R2_001.fastq.gz	fastq fastq	4696383909.0	39465411.0	GSM8287438 r16	0:28 1:91	A:1313674940;C:1038514326;G:1093116030;T:1250967700;N:110913	28	91	1313674940	1038514326	1093116030	1250967700	110913	SRX24663080	SRS21398378	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32258	32258	SRR29141396	SRX24663080	SRS21398378	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 6	GSM8287438		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 6	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287438	GSM8287438: Unablated rgc:ntr day 6; Danio rerio; RNA Seq	GSM8287438 r1	GSM8287438	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH133_S49_L003_R1_001.fastq.gz TH133_S49_L003_R2_001.fastq.gz	fastq fastq	4935093863.0	41471377.0	GSM8287438 r2	0:28 1:91	A:1378860058;C:1094061046;G:1149630737;T:1312423104;N:118918	28	91	1378860058	1094061046	1149630737	1312423104	118918	SRX24663080	SRS21398378	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32259	32259	SRR29141397	SRX24663080	SRS21398378	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 6	GSM8287438		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 6	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287438	GSM8287438: Unablated rgc:ntr day 6; Danio rerio; RNA Seq	GSM8287438 r1	GSM8287438	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH133_S49_L004_R1_001.fastq.gz TH133_S49_L004_R2_001.fastq.gz	fastq fastq	4820025147.0	40504413.0	GSM8287438 r3	0:28 1:91	A:1348394661;C:1067282812;G:1121376379;T:1282869478;N:101817	28	91	1348394661	1067282812	1121376379	1282869478	101817	SRX24663080	SRS21398378	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32260	32260	SRR29141398	SRX24663080	SRS21398378	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 6	GSM8287438		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 6	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287438	GSM8287438: Unablated rgc:ntr day 6; Danio rerio; RNA Seq	GSM8287438 r1	GSM8287438	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH133_S50_L002_R1_001.fastq.gz TH133_S50_L002_R2_001.fastq.gz	fastq fastq	4931460079.0	41440841.0	GSM8287438 r4	0:28 1:91	A:1379937889;C:1089994166;G:1147241148;T:1314171218;N:115658	28	91	1379937889	1089994166	1147241148	1314171218	115658	SRX24663080	SRS21398378	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32261	32261	SRR29141399	SRX24663080	SRS21398378	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 6	GSM8287438		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 6	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287438	GSM8287438: Unablated rgc:ntr day 6; Danio rerio; RNA Seq	GSM8287438 r1	GSM8287438	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH133_S50_L003_R1_001.fastq.gz TH133_S50_L003_R2_001.fastq.gz	fastq fastq	5229270193.0	43943447.0	GSM8287438 r5	0:28 1:91	A:1458651163;C:1159571989;G:1220750194;T:1390173862;N:122985	28	91	1458651163	1159571989	1220750194	1390173862	122985	SRX24663080	SRS21398378	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32262	32262	SRR29141400	SRX24663080	SRS21398378	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 6	GSM8287438		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 6	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287438	GSM8287438: Unablated rgc:ntr day 6; Danio rerio; RNA Seq	GSM8287438 r1	GSM8287438	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH133_S51_L001_R1_001.fastq.gz TH133_S51_L001_R2_001.fastq.gz	fastq fastq	4636122190.0	38959010.0	GSM8287438 r6	0:28 1:91	A:1298955001;C:1023834288;G:1079293988;T:1233918757;N:120156	28	91	1298955001	1023834288	1079293988	1233918757	120156	SRX24663080	SRS21398378	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32263	32263	SRR29141401	SRX24663080	SRS21398378	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 6	GSM8287438		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 6	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287438	GSM8287438: Unablated rgc:ntr day 6; Danio rerio; RNA Seq	GSM8287438 r1	GSM8287438	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH133_S51_L002_R1_001.fastq.gz TH133_S51_L002_R2_001.fastq.gz	fastq fastq	4651974894.0	39092226.0	GSM8287438 r7	0:28 1:91	A:1304274716;C:1026606682;G:1081394365;T:1239588507;N:110624	28	91	1304274716	1026606682	1081394365	1239588507	110624	SRX24663080	SRS21398378	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32264	32264	SRR29141402	SRX24663080	SRS21398378	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 6	GSM8287438		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 6	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287438	GSM8287438: Unablated rgc:ntr day 6; Danio rerio; RNA Seq	GSM8287438 r1	GSM8287438	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH133_S51_L004_R1_001.fastq.gz TH133_S51_L004_R2_001.fastq.gz	fastq fastq	4797101463.0	40311777.0	GSM8287438 r8	0:28 1:91	A:1341600660;C:1061361282;G:1117958236;T:1276080791;N:100494	28	91	1341600660	1061361282	1117958236	1276080791	100494	SRX24663080	SRS21398378	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32265	32265	SRR29141403	SRX24663080	SRS21398378	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 6	GSM8287438		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 6	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287438	GSM8287438: Unablated rgc:ntr day 6; Danio rerio; RNA Seq	GSM8287438 r1	GSM8287438	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH133_S52_L001_R1_001.fastq.gz TH133_S52_L001_R2_001.fastq.gz	fastq fastq	4697283787.0	39472973.0	GSM8287438 r9	0:28 1:91	A:1312647560;C:1039809509;G:1095056786;T:1249648802;N:121130	28	91	1312647560	1039809509	1095056786	1249648802	121130	SRX24663080	SRS21398378	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32266	32266	SRR29141404	SRX24663079	SRS21398377	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 7	GSM8287436		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 7	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287436	GSM8287436: Unablated rgc:ntr day 7; Danio rerio; RNA Seq	GSM8287436 r1	GSM8287436	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH110_S62_R1_001.fastq.gz TH110_S62_R2_001.fastq.gz	fastq fastq	7832538588.0	65819652.0	GSM8287436 r1	0:28 1:91	A:2264636103;C:1687265841;G:1826367106;T:2032749605;N:21519933	28	91	2264636103	1687265841	1826367106	2032749605	21519933	SRX24663079	SRS21398377	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32267	32267	SRR29141405	SRX24663079	SRS21398377	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 7	GSM8287436		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 7	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287436	GSM8287436: Unablated rgc:ntr day 7; Danio rerio; RNA Seq	GSM8287436 r1	GSM8287436	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH110_S63_R1_001.fastq.gz TH110_S63_R2_001.fastq.gz	fastq fastq	166170767.0	1396393.0	GSM8287436 r2	0:28 1:91	A:48248797;C:35717941;G:38752344;T:42997083;N:454602	28	91	48248797	35717941	38752344	42997083	454602	SRX24663079	SRS21398377	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	Larval	Eye	Sensory System
32268	32268	SRR29141406	SRX24663079	SRS21398377	SRP509393	PRJNA1115053	Large scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific	GSE268179	Other	Many genes are known to regulate Müller glia MG dependent retinal regeneration following widespread tissue damage. Conversely genes controlling regeneration following limited retinal cell loss per degenerative disease are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here transgenic zebrafish enabling inducible selective retinal ganglion cell RGC ablation were combined with single cell multiomics and CRISPR/Cas9 based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration and seven of these knockouts actually enhanced RGC replacement kinetics including sox2 olig2 and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e. biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem like state and context specificity in how genes function during regeneration. Increased understanding of how disease relevant cell types can be selectively regenerated will support the development of disease tailored regenerative therapeutics. Overall design: We performed single cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells RGCs 4 timepoints and ablation of rod photoreceptors and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.		pubmed:39007397		Unablated rgc:ntr day 7	GSM8287436		source name:Eye\|tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz\|geo loc name:missing\|collection date:missing	Unablated rgc:ntr day 7	scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline v4.3.0.1 and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly the top 2 000 variable genes were identified and used to identify principal components PCs of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes DEGs were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster minimum log2 foldchange cutoff of 0.25. scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC seq reads was performed using MACS2 in the ArchR package v1.0.2. ATAC seq data was then processed using the pbmc scATAC seq workflow with the Signac v1.10.0 and Seurat v4.3.0.1 packages for quality control normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next the ChromVar package v1.18.0 was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells. Assembly: GRCz11 Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files	Eye	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.	tissue:Eye\|transgenic line:rgc:ntr\|treatment:no mtz	GSM8287436	GSM8287436: Unablated rgc:ntr day 7; Danio rerio; RNA Seq	GSM8287436 r1	GSM8287436	1	scRNAseq: 40 60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain 10 eyes per 1 ml Worthington and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin Sigma Aldrich and 10 U/ml DNaseI Roche. Cells were filtered through a 70 μm filter Miltenyi Biotec kept on ice until 10X genomics processing. scMultiomeseq: 40 60 eyes were dissected and flash frozen in dry ice for 15min before being transferred to a 80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression GEX protocol CGOOO338. Briefly frozen retinal tissues were lysed in ice cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of 3000 5000 nuclei/ml and kept on ice until 10x genomics processing. Library preparation was then performed according to 10x genomics protocols.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP509393		loader:fastq load.py	TH110_S61_R1_001.fastq.gz TH110_S61_R2_001.fastq.gz	fastq fastq	8485930460.0	71310340.0	GSM8287436 r3	0:28 1:91	A:2462428503;C:1828880092;G:1970877358;T:2200821838;N:22922669	28	91	2462428503	1828880092	1970877358	2200821838	22922669	SRX24663079	SRS21398377	SRA1875751	Jeff Mumm, Ophthalmology, Johns Hopkins University	Jeff Mumm, Ophthalmology, Johns Hopkins University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-05-23	Undetermined	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");;