metadata: run_metadata: 32 rows where experiment.library_selection = "Oligo-dT", technology = "unknown" and tissue

32 rows where experiment.library_selection = "Oligo-dT", technology = "unknown" and tissue_curation = "Eye"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	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
30230	30230	SRR27730907	SRX23396554	SRS20257429	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		4dpi40Hz+biological replicate 2		4dpi40Hz 2		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:10\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165700aR1AL1A	M23165700aR1AL1A	4 xxx post injury+40Hz			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			4dpi40Hz_2_1.fq.gz 4dpi40Hz_2_2.fq.gz	fastq fastq	7794055500.0	25980185.0	4dpi40Hz 2 1.fq.gz	0:150 1:150	A:2129184357;C:1759642251;G:1791618685;T:2113568820;N:41387	150	150	2129184357	1759642251	1791618685	2113568820	41387	SRX23396554	SRS20257429	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
30231	30231	SRR27730908	SRX23396553	SRS20257428	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		4dpi40Hz+biological replicate 1		4dpi40Hz 1		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:9\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165699aR1AL1A	M23165699aR1AL1A	4 xxx post injury+40Hz			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			4dpi40Hz_1_1.fq.gz 4dpi40Hz_1_2.fq.gz	fastq fastq	7508652600.0	25028842.0	4dpi40Hz 1 1.fq.gz	0:150 1:150	A:2057198043;C:1689714910;G:1722042670;T:2039656491;N:40486	150	150	2057198043	1689714910	1722042670	2039656491	40486	SRX23396553	SRS20257428	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
30232	30232	SRR27730909	SRX23396552	SRS20257427	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		4dpi+biological replicate 4		4dpi 4		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:8\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165697aR1AL1A	M23165697aR1AL1A	4 xxx post injury			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			4dpi_4_1.fq.gz 4dpi_4_2.fq.gz	fastq fastq	7094977200.0	23649924.0	4dpi 4 1.fq.gz	0:150 1:150	A:1943019606;C:1597025881;G:1626301543;T:1928592039;N:38131	150	150	1943019606	1597025881	1626301543	1928592039	38131	SRX23396552	SRS20257427	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
30233	30233	SRR27730910	SRX23396551	SRS20257426	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		4dpi+biological replicate 3		4dpi 3		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:7\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165696aR1AL1A	M23165696aR1AL1A	4 xxx post injury			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			4dpi_3_1.fq.gz 4dpi_3_2.fq.gz	fastq fastq	7386629700.0	24622099.0	4dpi 3 1.fq.gz	0:150 1:150	A:2031801635;C:1655982922;G:1683647412;T:2015157737;N:39994	150	150	2031801635	1655982922	1683647412	2015157737	39994	SRX23396551	SRS20257426	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
30234	30234	SRR27730911	SRX23396550	SRS20257425	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		4dpi+biological replicate 2		4dpi 2		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:6\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165695aR1AL1A	M23165695aR1AL1A	4 xxx post injury			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			4dpi_2_1.fq.gz 4dpi_2_2.fq.gz	fastq fastq	6654237600.0	22180792.0	4dpi 2 1.fq.gz	0:150 1:150	A:1825547718;C:1496727215;G:1522459901;T:1809467151;N:35615	150	150	1825547718	1496727215	1522459901	1809467151	35615	SRX23396550	SRS20257425	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
30235	30235	SRR27730912	SRX23396549	SRS20257424	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		4dpi+biological replicate 1		4dpi 1		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:5\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165694aR1AL1A	M23165694aR1AL1A	4 xxx post injury			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			4dpi_1_1.fq.gz 4dpi_1_2.fq.gz	fastq fastq	7023034200.0	23410114.0	4dpi 1 1.fq.gz	0:150 1:150	A:1928523555;C:1581982138;G:1606070304;T:1906420119;N:38084	150	150	1928523555	1581982138	1606070304	1906420119	38084	SRX23396549	SRS20257424	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
30236	30236	SRR27730913	SRX23396548	SRS20257423	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		Con+biological replicate 4		Con 4		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:4\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165693aR1AL1A	M23165693aR1AL1A	Control			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			Con_4_1.fq.gz Con_4_2.fq.gz	fastq fastq	6857548800.0	22858496.0	Con 4 1.fq.gz	0:150 1:150	A:1882601360;C:1546021101;G:1569334195;T:1859555495;N:36649	150	150	1882601360	1546021101	1569334195	1859555495	36649	SRX23396548	SRS20257423	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
30237	30237	SRR27730914	SRX23396547	SRS20257422	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		Con+biological replicate 3		Con 3		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:3\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165692aR1AL1A	M23165692aR1AL1A	Control			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			Con_3_1.fq.gz Con_3_2.fq.gz	fastq fastq	7458957900.0	24863193.0	Con 3 1.fq.gz	0:150 1:150	A:2038911157;C:1679971639;G:1712675120;T:2027359083;N:40901	150	150	2038911157	1679971639	1712675120	2027359083	40901	SRX23396547	SRS20257422	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
30238	30238	SRR27730915	SRX23396546	SRS20257421	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		7dpi40Hz+biological replicate 4		7dpi40Hz 4		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:20\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165713aR1AL1A	M23165713aR1AL1A	7 xxx post injury+40Hz			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			7dpi40Hz_4_1.fq.gz 7dpi40Hz_4_2.fq.gz	fastq fastq	6691700400.0	22305668.0	7dpi40Hz 4 1.fq.gz	0:150 1:150	A:1868931421;C:1476540468;G:1501092489;T:1845097964;N:38058	150	150	1868931421	1476540468	1501092489	1845097964	38058	SRX23396546	SRS20257421	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
30239	30239	SRR27730916	SRX23396545	SRS20257420	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		7dpi40Hz+biological replicate 3		7dpi40Hz 3		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:19\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165712aR1AL1A	M23165712aR1AL1A	7 xxx post injury+40Hz			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			7dpi40Hz_3_1.fq.gz 7dpi40Hz_3_2.fq.gz	fastq fastq	7212117000.0	24040390.0	7dpi40Hz 3 1.fq.gz	0:150 1:150	A:1992256057;C:1607062903;G:1637554739;T:1975202488;N:40813	150	150	1992256057	1607062903	1637554739	1975202488	40813	SRX23396545	SRS20257420	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
30240	30240	SRR27730917	SRX23396544	SRS20257419	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		7dpi40Hz+biological replicate 2		7dpi40Hz 2		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:18\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165711aR1AL1A	M23165711aR1AL1A	7 xxx post injury+40Hz			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			7dpi40Hz_2_1.fq.gz 7dpi40Hz_2_2.fq.gz	fastq fastq	7457525100.0	24858417.0	7dpi40Hz 2 1.fq.gz	0:150 1:150	A:2040191437;C:1678135313;G:1713456206;T:2025700956;N:41188	150	150	2040191437	1678135313	1713456206	2025700956	41188	SRX23396544	SRS20257419	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
30241	30241	SRR27730918	SRX23396543	SRS20257418	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		7dpi40Hz+biological replicate 1		7dpi40Hz 1		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:17\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165710aR1AL1A	M23165710aR1AL1A	7 xxx post injury+40Hz			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			7dpi40Hz_1_1.fq.gz 7dpi40Hz_1_2.fq.gz	fastq fastq	6855385800.0	22851286.0	7dpi40Hz 1 1.fq.gz	0:150 1:150	A:1880374717;C:1545013977;G:1569663640;T:1860295686;N:37780	150	150	1880374717	1545013977	1569663640	1860295686	37780	SRX23396543	SRS20257418	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
30242	30242	SRR27730919	SRX23396542	SRS20257417	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		7dpi+biological replicate 4		7dpi 4		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:16\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165708aR1AL1A	M23165708aR1AL1A	7 xxx post injury			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			7dpi_4_1.fq.gz 7dpi_4_2.fq.gz	fastq fastq	6462470400.0	21541568.0	7dpi 4 1.fq.gz	0:150 1:150	A:1785795783;C:1441222995;G:1466593271;T:1768826748;N:31603	150	150	1785795783	1441222995	1466593271	1768826748	31603	SRX23396542	SRS20257417	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
30243	30243	SRR27730920	SRX23396541	SRS20257416	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		7dpi+biological replicate 3		7dpi 3		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:15\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165706aR1AL1A	M23165706aR1AL1A	7 xxx post injury			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			7dpi_3_1.fq.gz 7dpi_3_2.fq.gz	fastq fastq	6710491200.0	22368304.0	7dpi 3 1.fq.gz	0:150 1:150	A:1831876501;C:1512529252;G:1544827061;T:1821200080;N:58306	150	150	1831876501	1512529252	1544827061	1821200080	58306	SRX23396541	SRS20257416	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
30244	30244	SRR27730921	SRX23396540	SRS20257415	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		7dpi+biological replicate 2		7dpi 2		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:14\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165705aR1AL1A	M23165705aR1AL1A	7 xxx post injury			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			7dpi_2_1.fq.gz 7dpi_2_2.fq.gz	fastq fastq	6294917700.0	20983059.0	7dpi 2 1.fq.gz	0:150 1:150	A:1735431442;C:1394112982;G:1431966224;T:1733339379;N:67673	150	150	1735431442	1394112982	1431966224	1733339379	67673	SRX23396540	SRS20257415	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
30245	30245	SRR27730922	SRX23396539	SRS20257414	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		7dpi+biological replicate 1		7dpi 1		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:13\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165704aR1AL1A	M23165704aR1AL1A	7 xxx post injury			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			7dpi_1_1.fq.gz 7dpi_1_2.fq.gz	fastq fastq	6694150800.0	22313836.0	7dpi 1 1.fq.gz	0:150 1:150	A:1824840998;C:1510909671;G:1543521247;T:1814842377;N:36507	150	150	1824840998	1510909671	1543521247	1814842377	36507	SRX23396539	SRS20257414	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
30246	30246	SRR27730923	SRX23396538	SRS20257413	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		4dpi40Hz+biological replicate 4		4dpi40Hz 4		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:12\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165702aR1AL1A	M23165702aR1AL1A	4 xxx post injury+40Hz			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			4dpi40Hz_4_1.fq.gz 4dpi40Hz_4_2.fq.gz	fastq fastq	8672814300.0	28909381.0	4dpi40Hz 4 1.fq.gz	0:150 1:150	A:2372923011;C:1956760768;G:1989924842;T:2353159305;N:46374	150	150	2372923011	1956760768	1989924842	2353159305	46374	SRX23396538	SRS20257413	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
30247	30247	SRR27730924	SRX23396537	SRS20257412	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		4dpi40Hz+biological replicate 3		4dpi40Hz 3		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:11\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165701aR1AL1A	M23165701aR1AL1A	4 xxx post injury+40Hz			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			4dpi40Hz_3_1.fq.gz 4dpi40Hz_3_2.fq.gz	fastq fastq	7566042300.0	25220141.0	4dpi40Hz 3 1.fq.gz	0:150 1:150	A:2073697374;C:1705150021;G:1733548148;T:2053605856;N:40901	150	150	2073697374	1705150021	1733548148	2053605856	40901	SRX23396537	SRS20257412	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
30248	30248	SRR27730925	SRX23396536	SRS20257411	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		Con+biological replicate 2		Con 2		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:2\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165691aR1AL1A	M23165691aR1AL1A	Control			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			Con_2_1.fq.gz Con_2_2.fq.gz	fastq fastq	7211639400.0	24038798.0	Con 2 1.fq.gz	0:150 1:150	A:1979869383;C:1617364490;G:1649637969;T:1964729059;N:38499	150	150	1979869383	1617364490	1649637969	1964729059	38499	SRX23396536	SRS20257411	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
30249	30249	SRR27730926	SRX23396535	SRS20257410	SRP486007	PRJNA1069290	Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish	PRJNA1069290	Other	In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.		Con+biological replicate 1		Con 1		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month 6 month\|dev stage:3 month 6 month\|collection date:2023 07\|geo loc name:China:Nanchang\|sex:pooled male and female\|tissue:retina\|ID:1\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: retina	M23165689aR1AL1A	M23165689aR1AL1A	Control			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486007			Con_1_1.fq.gz Con_1_2.fq.gz	fastq fastq	6217369800.0	20724566.0	Con 1 1.fq.gz	0:150 1:150	A:1714156006;C:1391042352;G:1415307378;T:1696831326;N:32738	150	150	1714156006	1391042352	1415307378	1696831326	32738	SRX23396535	SRS20257410	SRA1791874	Affiliated Eye Hospital of Nanchang University\|Department of Ophthalmology	Affiliated Eye Hospital of Nanchang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-01-25	Adult	Adult	Eye	Sensory System
67572	67572	SRR17224783	SRX13404158	SRS11307154	SRP350669	PRJNA788440	Danio rerio Raw sequence reads	PRJNA788440	Whole Genome Sequencing	Danio rerio Raw sequence reads of eyes and skin				zebrafisheye		breed:AB\|age:30days\|sex:pooled male and female\|tissue:eyes\|BioSampleModel:Model organism or animal	RNAseq of zebrafish	eye mut 1 30dpf	eye mut 1 30dpf	RNAseq of eye			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350669			eye_mut_1_30dpf.R1.fastq.gz eye_mut_1_30dpf.R2.fastq.gz	fastq fastq	6647236232.0	22010716.0	eye mut 1 30dpf.R1.fastq.gz	0:151 1:151	A:1828748374;C:1496039359;G:1520471614;T:1801966254;N:10631	151	151	1828748374	1496039359	1520471614	1801966254	10631	SRX13404158	SRS11307154	SRA1343194	Huazhong Agricultural University\|College of Fisheries	Huazhong Agricultural University	2	0.91773	0.91812	0.11227	0.11178	0.6687	0.66931	0.47877	0.47805	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-12-14	Juvenile	Juvenile	Eye	Sensory System
67573	67573	SRR17224784	SRX13404157	SRS11307154	SRP350669	PRJNA788440	Danio rerio Raw sequence reads	PRJNA788440	Whole Genome Sequencing	Danio rerio Raw sequence reads of eyes and skin				zebrafisheye		breed:AB\|age:30days\|sex:pooled male and female\|tissue:eyes\|BioSampleModel:Model organism or animal	RNAseq of zebrafish	eye wt 3 30dpf	eye wt 3 30dpf	RNAseq of eye			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350669			eye_wt_3_30dpf.R1.fastq.gz eye_wt_3_30dpf.R2.fastq.gz	fastq fastq	6665043964.0	22069682.0	eye wt 3 30dpf.R1.fastq.gz	0:151 1:151	A:1837907813;C:1496332954;G:1517206099;T:1813585697;N:11401	151	151	1837907813	1496332954	1517206099	1813585697	11401	SRX13404157	SRS11307154	SRA1343194	Huazhong Agricultural University\|College of Fisheries	Huazhong Agricultural University	2	0.92328	0.92376	0.11972	0.11905	0.69002	0.69039	0.48654	0.48588	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-12-14	Juvenile	Juvenile	Eye	Sensory System
67574	67574	SRR17224785	SRX13404156	SRS11307154	SRP350669	PRJNA788440	Danio rerio Raw sequence reads	PRJNA788440	Whole Genome Sequencing	Danio rerio Raw sequence reads of eyes and skin				zebrafisheye		breed:AB\|age:30days\|sex:pooled male and female\|tissue:eyes\|BioSampleModel:Model organism or animal	RNAseq of zebrafish	eye wt 2 30dpf	eye wt 2 30dpf	RNAseq of eye			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350669			eye_wt_2_30dpf.R1.fastq.gz eye_wt_2_30dpf.R2.fastq.gz	fastq fastq	7313252536.0	24216068.0	eye wt 2 30dpf.R1.fastq.gz	0:151 1:151	A:2005760880;C:1644712229;G:1691008059;T:1971759242;N:12126	151	151	2005760880	1644712229	1691008059	1971759242	12126	SRX13404156	SRS11307154	SRA1343194	Huazhong Agricultural University\|College of Fisheries	Huazhong Agricultural University	2	0.92458	0.92267	0.11276	0.11098	0.68834	0.6939	0.48994	0.48977	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-12-14	Juvenile	Juvenile	Eye	Sensory System
67575	67575	SRR17224786	SRX13404155	SRS11307154	SRP350669	PRJNA788440	Danio rerio Raw sequence reads	PRJNA788440	Whole Genome Sequencing	Danio rerio Raw sequence reads of eyes and skin				zebrafisheye		breed:AB\|age:30days\|sex:pooled male and female\|tissue:eyes\|BioSampleModel:Model organism or animal	RNAseq of zebrafish	eye wt 1 30dpf	eye wt 1 30dpf	RNAseq of eye			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350669			eye_wt_1_30dpf.R1.fastq.gz eye_wt_1_30dpf.R2.fastq.gz	fastq fastq	7374231470.0	24417985.0	eye wt 1 30dpf.R1.fastq.gz	0:151 1:151	A:2032283041;C:1657026689;G:1681898985;T:2003011689;N:11066	151	151	2032283041	1657026689	1681898985	2003011689	11066	SRX13404155	SRS11307154	SRA1343194	Huazhong Agricultural University\|College of Fisheries	Huazhong Agricultural University	2	0.92217	0.92217	0.11433	0.11344	0.69045	0.69087	0.48935	0.47534	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-12-14	Juvenile	Juvenile	Eye	Sensory System
67580	67580	SRR17224791	SRX13404150	SRS11307154	SRP350669	PRJNA788440	Danio rerio Raw sequence reads	PRJNA788440	Whole Genome Sequencing	Danio rerio Raw sequence reads of eyes and skin				zebrafisheye		breed:AB\|age:30days\|sex:pooled male and female\|tissue:eyes\|BioSampleModel:Model organism or animal	RNAseq of zebrafish	eye mut 3 30dpf	eye mut 3 30dpf	RNAseq of eye			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350669			eye_mut_3_30dpf.R1.fastq.gz eye_mut_3_30dpf.R2.fastq.gz	fastq fastq	7370863566.0	24406833.0	eye mut 3 30dpf.R1.fastq.gz	0:151 1:151	A:2035593457;C:1650415961;G:1678944830;T:2005897248;N:12070	151	151	2035593457	1650415961	1678944830	2005897248	12070	SRX13404150	SRS11307154	SRA1343194	Huazhong Agricultural University\|College of Fisheries	Huazhong Agricultural University	2	0.9169	0.91717	0.11546	0.11616	0.66249	0.66312	0.47895	0.47697	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-12-14	Juvenile	Juvenile	Eye	Sensory System
67581	67581	SRR17224792	SRX13404149	SRS11307154	SRP350669	PRJNA788440	Danio rerio Raw sequence reads	PRJNA788440	Whole Genome Sequencing	Danio rerio Raw sequence reads of eyes and skin				zebrafisheye		breed:AB\|age:30days\|sex:pooled male and female\|tissue:eyes\|BioSampleModel:Model organism or animal	RNAseq of zebrafish	eye mut 2 30dpf	eye mut 2 30dpf	RNAseq of eye			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350669			eye_mut_2_30dpf.R1.fastq.gz eye_mut_2_30dpf.R2.fastq.gz	fastq fastq	6025971496.0	19953548.0	eye mut 2 30dpf.R1.fastq.gz	0:151 1:151	A:1659612510;C:1355527081;G:1377376165;T:1633446020;N:9720	151	151	1659612510	1355527081	1377376165	1633446020	9720	SRX13404149	SRS11307154	SRA1343194	Huazhong Agricultural University\|College of Fisheries	Huazhong Agricultural University	2	0.91909	0.92042	0.11187	0.11181	0.66884	0.66985	0.48856	0.49166	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-12-14	Juvenile	Juvenile	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");;