rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
2319,ERR1289947,ERX1361553,ERS954843,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647694,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:23:00Z|External Id:SAMEA3647694|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:23:00Z|INSDC status:public|Submitter Id:ATH5 2 sc 2454965|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:ATH5 2 sc 2454965|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#12,15249493,Illumina sequencing of library 15249493  constructed from sample accession ERS954843 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence TAGGCATGAGAGTAGA.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#12.cram,cram,2492206600.0,12461033.0,SC RUN 18222 2#12,0:100 1:100,A:661236051;C:588399772;G:571478215;T:671080581;N:11981,100,100,,,661236051,588399772,571478215,671080581,11981,ERX1361553,ERS954843,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94054,0.94077,0.10025,0.10255,0.75779,0.76019,0.4807,0.47966,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2320,ERR1289946,ERX1361552,ERS954842,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647693,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:23:00Z|External Id:SAMEA3647693|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:23:00Z|INSDC status:public|Submitter Id:WT ctrl sc 2454964|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:WT ctrl sc 2454964|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#11,15249492,Illumina sequencing of library 15249492  constructed from sample accession ERS954842 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence TAGGCATGTATCCTCT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#11.cram,cram,2748114600.0,13740573.0,SC RUN 18222 2#11,0:100 1:100,A:747132237;C:630918171;G:613637334;T:756413030;N:13828,100,100,,,747132237,630918171,613637334,756413030,13828,ERX1361552,ERS954842,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.91201,0.911,0.09071,0.09156,0.88994,0.88988,0.47118,0.49948,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2321,ERR1289945,ERX1361551,ERS954841,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647692,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:59Z|External Id:SAMEA3647692|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:59Z|INSDC status:public|Submitter Id:RX2 ATH5 GFP3 sc 2454963|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ATH5 GFP3 sc 2454963|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#10,15249491,Illumina sequencing of library 15249491  constructed from sample accession ERS954841 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence TAGGCATGCTCTCTAT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#10.cram,cram,3366968000.0,16834840.0,SC RUN 18222 2#10,0:100 1:100,A:881918684;C:806052916;G:790157920;T:888821188;N:17292,100,100,,,881918684,806052916,790157920,888821188,17292,ERX1361551,ERS954841,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94171,0.94098,0.0849,0.08607,0.74862,0.75024,0.50963,0.50955,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2322,ERR1289944,ERX1361550,ERS954840,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647691,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647691|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:RX2 ATH5 GFP2 sc 2454962|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ATH5 GFP2 sc 2454962|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#9,15249490,Illumina sequencing of library 15249490  constructed from sample accession ERS954840 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence TAGGCATGTAGATCGC.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#9.cram,cram,3222261000.0,16111305.0,SC RUN 18222 2#9,0:100 1:100,A:819997366;C:795302699;G:777099203;T:829845734;N:15998,100,100,,,819997366,795302699,777099203,829845734,15998,ERX1361550,ERS954840,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94529,0.94495,0.0603,0.06143,0.76157,0.76238,0.48847,0.4882,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2323,ERR1289943,ERX1361549,ERS954839,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647690,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647690|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 GFP2 high sc 2454961|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 GFP2 high sc 2454961|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#8,15249489,Illumina sequencing of library 15249489  constructed from sample accession ERS954839 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence GGACTCCTCTAAGCCT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#8.cram,cram,3834749800.0,19173749.0,SC RUN 18222 2#8,0:100 1:100,A:992673645;C:929008642;G:906766397;T:1006281701;N:19415,100,100,,,992673645,929008642,906766397,1006281701,19415,ERX1361549,ERS954839,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94351,0.94297,0.08055,0.08157,0.72853,0.73095,0.52148,0.51755,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2324,ERR1289942,ERX1361548,ERS954838,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647689,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647689|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 GFP2 low sc 2454960|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 GFP2 low sc 2454960|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#7,15249488,Illumina sequencing of library 15249488  constructed from sample accession ERS954838 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence GGACTCCTAAGGAGTA.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#7.cram,cram,1076581000.0,5382905.0,SC RUN 18222 2#7,0:100 1:100,A:285946062;C:254142940;G:242866633;T:293619980;N:5385,100,100,,,285946062,254142940,242866633,293619980,5385,ERX1361548,ERS954838,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.89818,0.89819,0.1022,0.10292,0.89919,0.89852,0.51448,0.51223,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2325,ERR1289941,ERX1361547,ERS954837,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647688,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647688|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:GFAP ATH5 GFP2 sc 2454959|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:GFAP ATH5 GFP2 sc 2454959|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#6,15249487,Illumina sequencing of library 15249487  constructed from sample accession ERS954837 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence GGACTCCTACTGCATA.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#6.cram,cram,3172834800.0,15864174.0,SC RUN 18222 2#6,0:100 1:100,A:841262183;C:748974758;G:730474017;T:852107947;N:15895,100,100,,,841262183,748974758,730474017,852107947,15895,ERX1361547,ERS954837,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.93515,0.93517,0.10079,0.10267,0.73403,0.73511,0.49831,0.47169,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2326,ERR1289940,ERX1361546,ERS954836,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647687,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647687|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:ATH5 1 sc 2454958|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:ATH5 1 sc 2454958|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#5,15249486,Illumina sequencing of library 15249486  constructed from sample accession ERS954836 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence GGACTCCTGTAAGGAG.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#5.cram,cram,1188728400.0,5943642.0,SC RUN 18222 2#5,0:100 1:100,A:322290258;C:273659598;G:266021599;T:326751009;N:5936,100,100,,,322290258,273659598,266021599,326751009,5936,ERX1361546,ERS954836,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.92438,0.92391,0.12338,0.1251,0.76288,0.76479,0.48734,0.47777,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2327,ERR1289939,ERX1361545,ERS954835,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647686,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647686|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:GFAP ATH5 GFP1 sc 2454957|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:GFAP ATH5 GFP1 sc 2454957|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#4,15249485,Illumina sequencing of library 15249485  constructed from sample accession ERS954835 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence GGACTCCTAGAGTAGA.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#4.cram,cram,2335470400.0,11677352.0,SC RUN 18222 2#4,0:100 1:100,A:611730664;C:560095252;G:541373953;T:622259122;N:11409,100,100,,,611730664,560095252,541373953,622259122,11409,ERX1361545,ERS954835,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.93481,0.93465,0.10573,0.10811,0.77135,0.77303,0.50016,0.50137,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2328,ERR1289938,ERX1361544,ERS954834,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647685,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647685|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 ATH5 GFP1 sc 2454956|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ATH5 GFP1 sc 2454956|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#3,15249484,Illumina sequencing of library 15249484  constructed from sample accession ERS954834 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence GGACTCCTTATCCTCT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#3.cram,cram,2932765000.0,14663825.0,SC RUN 18222 2#3,0:100 1:100,A:762543647;C:708033363;G:692599413;T:769573475;N:15102,100,100,,,762543647,708033363,692599413,769573475,15102,ERX1361544,ERS954834,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94442,0.94374,0.07322,0.07439,0.74383,0.74531,0.50604,0.51608,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2329,ERR1289937,ERX1361543,ERS954833,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647684,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:15Z|External Id:SAMEA3647684|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:15Z|INSDC status:public|Submitter Id:RX2 GFP1 sc 2454955|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 GFP1 sc 2454955|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#2,15249483,Illumina sequencing of library 15249483  constructed from sample accession ERS954833 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence GGACTCCTCTCTCTAT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#2.cram,cram,2432398000.0,12161990.0,SC RUN 18222 2#2,0:100 1:100,A:624543123;C:594774023;G:581130641;T:631937939;N:12274,100,100,,,624543123,594774023,581130641,631937939,12274,ERX1361543,ERS954833,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94225,0.94103,0.08221,0.0823,0.79289,0.79383,0.51106,0.5129,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2330,ERR1289936,ERX1361542,ERS954832,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647683,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647683|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 ctrl noGFP sc 2454954|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ctrl noGFP sc 2454954|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#1,15249482,Illumina sequencing of library 15249482  constructed from sample accession ERS954832 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence GGACTCCTTAGATCGC.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#1.cram,cram,361900800.0,1809504.0,SC RUN 18222 2#1,0:100 1:100,A:84553945;C:97259075;G:92615955;T:87470072;N:1753,100,100,,,84553945,97259075,92615955,87470072,1753,ERX1361542,ERS954832,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94897,0.95014,0.07743,0.07772,0.71969,0.72058,0.43784,0.44067,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2331,ERR1289935,ERX1361541,ERS954843,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647694,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:23:00Z|External Id:SAMEA3647694|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:23:00Z|INSDC status:public|Submitter Id:ATH5 2 sc 2454965|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:ATH5 2 sc 2454965|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#12,15249493,Illumina sequencing of library 15249493  constructed from sample accession ERS954843 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence TAGGCATGAGAGTAGA.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#12.cram,cram,2487554200.0,12437771.0,SC RUN 18222 1#12,0:100 1:100,A:660028585;C:587257902;G:570415230;T:669842822;N:9661,100,100,,,660028585,587257902,570415230,669842822,9661,ERX1361541,ERS954843,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94059,0.9397,0.09914,0.1011,0.75597,0.75862,0.48558,0.48548,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2332,ERR1289934,ERX1361540,ERS954842,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647693,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:23:00Z|External Id:SAMEA3647693|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:23:00Z|INSDC status:public|Submitter Id:WT ctrl sc 2454964|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:WT ctrl sc 2454964|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#11,15249492,Illumina sequencing of library 15249492  constructed from sample accession ERS954842 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence TAGGCATGTATCCTCT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#11.cram,cram,2740851200.0,13704256.0,SC RUN 18222 1#11,0:100 1:100,A:745054545;C:629082779;G:612051041;T:754652050;N:10785,100,100,,,745054545,629082779,612051041,754652050,10785,ERX1361540,ERS954842,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.91349,0.91229,0.09216,0.09351,0.88962,0.89043,0.48978,0.5028,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2333,ERR1289933,ERX1361539,ERS954841,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647692,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:59Z|External Id:SAMEA3647692|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:59Z|INSDC status:public|Submitter Id:RX2 ATH5 GFP3 sc 2454963|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ATH5 GFP3 sc 2454963|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#10,15249491,Illumina sequencing of library 15249491  constructed from sample accession ERS954841 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence TAGGCATGCTCTCTAT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#10.cram,cram,3357950400.0,16789752.0,SC RUN 18222 1#10,0:100 1:100,A:879637755;C:803810252;G:787961249;T:886528291;N:12853,100,100,,,879637755,803810252,787961249,886528291,12853,ERX1361539,ERS954841,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94064,0.94017,0.08377,0.08517,0.74909,0.75136,0.50723,0.50903,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2334,ERR1289932,ERX1361538,ERS954840,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647691,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647691|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:RX2 ATH5 GFP2 sc 2454962|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ATH5 GFP2 sc 2454962|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#9,15249490,Illumina sequencing of library 15249490  constructed from sample accession ERS954840 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence TAGGCATGTAGATCGC.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#9.cram,cram,3206581200.0,16032906.0,SC RUN 18222 1#9,0:100 1:100,A:816111545;C:791236086;G:773298814;T:825922398;N:12357,100,100,,,816111545,791236086,773298814,825922398,12357,ERX1361538,ERS954840,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94549,0.94564,0.06037,0.06105,0.76043,0.76171,0.48313,0.49555,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2335,ERR1289931,ERX1361537,ERS954839,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647690,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647690|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 GFP2 high sc 2454961|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 GFP2 high sc 2454961|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#8,15249489,Illumina sequencing of library 15249489  constructed from sample accession ERS954839 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence GGACTCCTCTAAGCCT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#8.cram,cram,3822332200.0,19111661.0,SC RUN 18222 1#8,0:100 1:100,A:989542225;C:925823012;G:903835738;T:1003115980;N:15245,100,100,,,989542225,925823012,903835738,1003115980,15245,ERX1361537,ERS954839,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94289,0.94174,0.07966,0.08004,0.72764,0.72906,0.51976,0.52464,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2336,ERR1289930,ERX1361536,ERS954838,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647689,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647689|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 GFP2 low sc 2454960|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 GFP2 low sc 2454960|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#7,15249488,Illumina sequencing of library 15249488  constructed from sample accession ERS954838 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence GGACTCCTAAGGAGTA.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#7.cram,cram,1072510200.0,5362551.0,SC RUN 18222 1#7,0:100 1:100,A:284863902;C:253046005;G:241968135;T:292627849;N:4309,100,100,,,284863902,253046005,241968135,292627849,4309,ERX1361536,ERS954838,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.89703,0.89873,0.10191,0.10317,0.89921,0.8984,0.50884,0.51319,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2337,ERR1289929,ERX1361535,ERS954837,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647688,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647688|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:GFAP ATH5 GFP2 sc 2454959|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:GFAP ATH5 GFP2 sc 2454959|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#6,15249487,Illumina sequencing of library 15249487  constructed from sample accession ERS954837 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence GGACTCCTACTGCATA.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#6.cram,cram,3159715800.0,15798579.0,SC RUN 18222 1#6,0:100 1:100,A:837700548;C:745877706;G:727508293;T:848616717;N:12536,100,100,,,837700548,745877706,727508293,848616717,12536,ERX1361535,ERS954837,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.93397,0.93362,0.10011,0.10205,0.73474,0.73612,0.49003,0.49085,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2338,ERR1289928,ERX1361534,ERS954836,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647687,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647687|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:ATH5 1 sc 2454958|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:ATH5 1 sc 2454958|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#5,15249486,Illumina sequencing of library 15249486  constructed from sample accession ERS954836 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence GGACTCCTGTAAGGAG.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#5.cram,cram,1184332600.0,5921663.0,SC RUN 18222 1#5,0:100 1:100,A:321129432;C:272595945;G:264945795;T:325656767;N:4661,100,100,,,321129432,272595945,264945795,325656767,4661,ERX1361534,ERS954836,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.92372,0.92353,0.12445,0.12616,0.76339,0.76495,0.48995,0.48259,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2339,ERR1289927,ERX1361533,ERS954835,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647686,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647686|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:GFAP ATH5 GFP1 sc 2454957|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:GFAP ATH5 GFP1 sc 2454957|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#4,15249485,Illumina sequencing of library 15249485  constructed from sample accession ERS954835 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence GGACTCCTAGAGTAGA.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#4.cram,cram,2331489600.0,11657448.0,SC RUN 18222 1#4,0:100 1:100,A:610715735;C:559128165;G:540406653;T:621229940;N:9107,100,100,,,610715735,559128165,540406653,621229940,9107,ERX1361533,ERS954835,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.9338,0.93348,0.10518,0.10783,0.77155,0.77374,0.49506,0.49808,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2340,ERR1289926,ERX1361532,ERS954834,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647685,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647685|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 ATH5 GFP1 sc 2454956|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ATH5 GFP1 sc 2454956|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#3,15249484,Illumina sequencing of library 15249484  constructed from sample accession ERS954834 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence GGACTCCTTATCCTCT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#3.cram,cram,2923134800.0,14615674.0,SC RUN 18222 1#3,0:100 1:100,A:760057089;C:705694497;G:690249046;T:767122385;N:11783,100,100,,,760057089,705694497,690249046,767122385,11783,ERX1361532,ERS954834,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94509,0.94377,0.07431,0.07512,0.74367,0.74525,0.50981,0.51595,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2341,ERR1289925,ERX1361531,ERS954833,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647684,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:15Z|External Id:SAMEA3647684|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:15Z|INSDC status:public|Submitter Id:RX2 GFP1 sc 2454955|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 GFP1 sc 2454955|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#2,15249483,Illumina sequencing of library 15249483  constructed from sample accession ERS954833 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence GGACTCCTCTCTCTAT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#2.cram,cram,2423614200.0,12118071.0,SC RUN 18222 1#2,0:100 1:100,A:622254096;C:592596967;G:579007199;T:629746522;N:9416,100,100,,,622254096,592596967,579007199,629746522,9416,ERX1361531,ERS954833,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94151,0.94151,0.08127,0.08228,0.79091,0.79235,0.51421,0.50953,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2342,ERR1289924,ERX1361530,ERS954832,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647683,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647683|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 ctrl noGFP sc 2454954|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ctrl noGFP sc 2454954|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#1,15249482,Illumina sequencing of library 15249482  constructed from sample accession ERS954832 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence GGACTCCTTAGATCGC.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#1.cram,cram,359779800.0,1798899.0,SC RUN 18222 1#1,0:100 1:100,A:84065568;C:96668644;G:92071125;T:86973168;N:1295,100,100,,,84065568,96668644,92071125,86973168,1295,ERX1361530,ERS954832,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.9502,0.9506,0.07759,0.07791,0.71772,0.71827,0.44568,0.45005,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
29092,SRR27010839,SRX22703628,SRS19696103,SRP475450,PRJNA1047749,Differential expression in Muller glia of injured zebrafish in a mycb /  context,GSE249116,Transcriptome Analysis,This experiment studies retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mycb /  Muller glia from injured mycb /  fish at 2dpi.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from mycb /  retinas 2 xxx post injury dpi rep2 [7131 ML 8] [7131 ML 8],GSM7926876,,source name:mycb /  Muller glia injured retina|tissue:mycb /  Muller glia injured retina|genotype:mycb / |treatment:injured|geo loc name:missing|collection date:missing,Muller glia from mycb /  retinas 2 xxx post injury dpi rep2 [7131 ML 8] [7131 ML 8],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS11 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",mycb /  Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:mycb /  Muller glia injured retina|genotype:mycb / |treatment:injured,GSM7926876,GSM7926876: Muller glia from mycb /  retinas 2 xxx post injury dpi rep2 [7131 ML 8] [7131 ML 8]; Danio rerio; RNA Seq,GSM7926876 r1,GSM7926876,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475450,,loader:fastq load.py,7131-ML-8_GCTGGCCA-GCGTCCGT_S74_R1_001.fastq.gz 7131-ML-8_GCTGGCCA-GCGTCCGT_S74_R2_001.fastq.gz,fastq fastq,27012387282.0,89444991.0,GSM7926876 r1,0:151 1:151,A:7324891140;C:5760958085;G:6796293318;T:7129968103;N:276636,151,151,,,7324891140,5760958085,6796293318,7129968103,276636,SRX22703628,SRS19696103,SRA1761650,University of Michigan,University of Michigan,2,0.88985,0.86096,0.09217,0.08056,0.7473,0.7542,0.59862,0.5926,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29093,SRR27010840,SRX22703627,SRS19696102,SRP475450,PRJNA1047749,Differential expression in Muller glia of injured zebrafish in a mycb /  context,GSE249116,Transcriptome Analysis,This experiment studies retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mycb /  Muller glia from injured mycb /  fish at 2dpi.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from mycb /  retinas 2 xxx post injury dpi rep1 [7131 ML 7] [7131 ML 7],GSM7926875,,source name:mycb /  Muller glia injured retina|tissue:mycb /  Muller glia injured retina|genotype:mycb / |treatment:injured|geo loc name:missing|collection date:missing,Muller glia from mycb /  retinas 2 xxx post injury dpi rep1 [7131 ML 7] [7131 ML 7],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS11 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",mycb /  Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:mycb /  Muller glia injured retina|genotype:mycb / |treatment:injured,GSM7926875,GSM7926875: Muller glia from mycb /  retinas 2 xxx post injury dpi rep1 [7131 ML 7] [7131 ML 7]; Danio rerio; RNA Seq,GSM7926875 r1,GSM7926875,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475450,,loader:fastq load.py,7131-ML-7_TTACGGAC-ATTGGCCA_S73_R1_001.fastq.gz 7131-ML-7_TTACGGAC-ATTGGCCA_S73_R2_001.fastq.gz,fastq fastq,27084816546.0,89684823.0,GSM7926875 r1,0:151 1:151,A:7489987820;C:5729672678;G:6569226079;T:7295655071;N:274898,151,151,,,7489987820,5729672678,6569226079,7295655071,274898,SRX22703627,SRS19696102,SRA1761650,University of Michigan,University of Michigan,2,0.8887,0.84473,0.12952,0.10995,0.73338,0.74211,0.54826,0.56906,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29094,SRR27010841,SRX22703626,SRS19696101,SRP475450,PRJNA1047749,Differential expression in Muller glia of injured zebrafish in a mycb /  context,GSE249116,Transcriptome Analysis,This experiment studies retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mycb /  Muller glia from injured mycb /  fish at 2dpi.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from WT retinas 2 xxx post injury dpi rep2 [7131 ML 5] [7131 ML 5],GSM7926874,,source name:WT Muller glia injured retina|tissue:WT Muller glia injured retina|genotype:WT|treatment:n1|geo loc name:missing|collection date:missing,Muller glia from WT retinas 2 xxx post injury dpi rep2 [7131 ML 5] [7131 ML 5],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS11 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller glia injured retina|genotype:WT|treatment:n1,GSM7926874,GSM7926874: Muller glia from WT retinas 2 xxx post injury dpi rep2 [7131 ML 5] [7131 ML 5]; Danio rerio; RNA Seq,GSM7926874 r1,GSM7926874,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475450,,loader:fastq load.py,7131-ML-5_CAACCATA-ACCGGTTA_S71_R1_001.fastq.gz 7131-ML-5_CAACCATA-ACCGGTTA_S71_R2_001.fastq.gz,fastq fastq,29094896836.0,96340718.0,GSM7926874 r1,0:151 1:151,A:7739727136;C:6356741244;G:7473778902;T:7524355633;N:293921,151,151,,,7739727136,6356741244,7473778902,7524355633,293921,SRX22703626,SRS19696101,SRA1761650,University of Michigan,University of Michigan,2,0.88966,0.85954,0.08909,0.07794,0.72711,0.73446,0.54596,0.54295,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29095,SRR27010842,SRX22703625,SRS19696100,SRP475450,PRJNA1047749,Differential expression in Muller glia of injured zebrafish in a mycb /  context,GSE249116,Transcriptome Analysis,This experiment studies retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mycb /  Muller glia from injured mycb /  fish at 2dpi.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from WT retinas 2 xxx post injury dpi rep1 [7131 ML 4] [7131 ML 4],GSM7926873,,source name:WT Muller glia injured retina|tissue:WT Muller glia injured retina|genotype:WT|treatment:n1|geo loc name:missing|collection date:missing,Muller glia from WT retinas 2 xxx post injury dpi rep1 [7131 ML 4] [7131 ML 4],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS11 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller glia injured retina|genotype:WT|treatment:n1,GSM7926873,GSM7926873: Muller glia from WT retinas 2 xxx post injury dpi rep1 [7131 ML 4] [7131 ML 4]; Danio rerio; RNA Seq,GSM7926873 r1,GSM7926873,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475450,,loader:fastq load.py,7131-ML-4_TTAACGGC-CTCCGTCT_S70_R1_001.fastq.gz 7131-ML-4_TTAACGGC-CTCCGTCT_S70_R2_001.fastq.gz,fastq fastq,36567606580.0,121084790.0,GSM7926873 r1,0:151 1:151,A:9477563071;C:8136361552;G:9699876329;T:9253435137;N:370491,151,151,,,9477563071,8136361552,9699876329,9253435137,370491,SRX22703625,SRS19696100,SRA1761650,University of Michigan,University of Michigan,2,0.85059,0.82538,0.08689,0.07693,0.73574,0.74371,0.54735,0.54664,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29096,SRR27010843,SRX22703624,SRS19696099,SRP475450,PRJNA1047749,Differential expression in Muller glia of injured zebrafish in a mycb /  context,GSE249116,Transcriptome Analysis,This experiment studies retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mycb /  Muller glia from injured mycb /  fish at 2dpi.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from uninjured WT retinas rep2 [7131 ML 2] [7131 ML 2],GSM7926872,,source name:WT Muller retinal glia|tissue:WT Muller retinal glia|genotype:WT|treatment:n1|geo loc name:missing|collection date:missing,Muller glia from uninjured WT retinas rep2 [7131 ML 2] [7131 ML 2],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS11 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller retinal glia,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller retinal glia|genotype:WT|treatment:n1,GSM7926872,GSM7926872: Muller glia from uninjured WT retinas rep2 [7131 ML 2] [7131 ML 2]; Danio rerio; RNA Seq,GSM7926872 r1,GSM7926872,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475450,,loader:fastq load.py,7131-ML-2_ACAGAGAA-GCGGTTAC_S68_R1_001.fastq.gz 7131-ML-2_ACAGAGAA-GCGGTTAC_S68_R2_001.fastq.gz,fastq fastq,31134149118.0,103093209.0,GSM7926872 r1,0:151 1:151,A:8551703439;C:6621403525;G:7636841163;T:8323884132;N:316859,151,151,,,8551703439,6621403525,7636841163,8323884132,316859,SRX22703624,SRS19696099,SRA1761650,University of Michigan,University of Michigan,2,0.89461,0.85335,0.11633,0.10042,0.74302,0.74943,0.5613,0.54558,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29097,SRR27010844,SRX22703623,SRS19696098,SRP475450,PRJNA1047749,Differential expression in Muller glia of injured zebrafish in a mycb /  context,GSE249116,Transcriptome Analysis,This experiment studies retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mycb /  Muller glia from injured mycb /  fish at 2dpi.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from uninjured WT retinas rep1 [7131 ML 1] [7131 ML 1],GSM7926871,,source name:WT Muller retinal glia|tissue:WT Muller retinal glia|genotype:WT|treatment:n1|geo loc name:missing|collection date:missing,Muller glia from uninjured WT retinas rep1 [7131 ML 1] [7131 ML 1],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS11 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller retinal glia,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller retinal glia|genotype:WT|treatment:n1,GSM7926871,GSM7926871: Muller glia from uninjured WT retinas rep1 [7131 ML 1] [7131 ML 1]; Danio rerio; RNA Seq,GSM7926871 r1,GSM7926871,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475450,,loader:fastq load.py,7131-ML-1_AATGTTGT-TGCTTACA_S67_R1_001.fastq.gz 7131-ML-1_AATGTTGT-TGCTTACA_S67_R2_001.fastq.gz,fastq fastq,30223430972.0,100077586.0,GSM7926871 r1,0:151 1:151,A:8370937172;C:6520369124;G:7146916733;T:8184902603;N:305340,151,151,,,8370937172,6520369124,7146916733,8184902603,305340,SRX22703623,SRS19696098,SRA1761650,University of Michigan,University of Michigan,2,0.91221,0.86081,0.12114,0.10476,0.73164,0.73882,0.54727,0.52951,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29098,SRR27010846,SRX22703638,SRS19696113,SRP475451,PRJNA1047750,Differential expression in Muller glia of injured zebrafish in a mych /  context,GSE249115,Transcriptome Analysis,This experiment studies  retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mych /  Muller glia from injured mych /  fish at 2dpi. Of interest are the WT injury responsive genes  and which injury responsive genes in the WT are differentially expressed in the mych /  fish.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from mych /  retinas 2 xxx post injury dpi rep3 [5803 ML 10],GSM7926870,,source name:mych /  Muller glia injured retina|tissue:mych /  Muller glia injured retina|genotype:mych / |treatment:injured|geo loc name:missing|collection date:missing,Muller glia from mych /  retinas 2 xxx post injury dpi rep3 [5803 ML 10],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",mych /  Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:mych /  Muller glia injured retina|genotype:mych / |treatment:injured,GSM7926870,GSM7926870: Muller glia from mych /  retinas 2 xxx post injury dpi rep3 [5803 ML 10]; Danio rerio; RNA Seq,GSM7926870 r1,GSM7926870,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475451,,loader:fastq load.py,5803-ML-10_AACAACGG-TTACACCT_S222_R1_001.fastq.gz 5803-ML-10_AACAACGG-TTACACCT_S222_R2_001.fastq.gz,fastq fastq,33066899590.0,109493045.0,GSM7926870 r1,0:151 1:151,A:9045925528;C:7063243555;G:8277253275;T:8680404068;N:73164,151,151,,,9045925528,7063243555,8277253275,8680404068,73164,SRX22703638,SRS19696113,SRA1761648,University of Michigan,University of Michigan,2,0.87174,0.82563,0.12217,0.10466,0.7052,0.71311,0.50335,0.51416,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29099,SRR27010847,SRX22703637,SRS19696112,SRP475451,PRJNA1047750,Differential expression in Muller glia of injured zebrafish in a mych /  context,GSE249115,Transcriptome Analysis,This experiment studies  retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mych /  Muller glia from injured mych /  fish at 2dpi. Of interest are the WT injury responsive genes  and which injury responsive genes in the WT are differentially expressed in the mych /  fish.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from mych /  retinas 2 xxx post injury dpi rep2 [5803 ML 8],GSM7926869,,source name:mych /  Muller glia injured retina|tissue:mych /  Muller glia injured retina|genotype:mych / |treatment:injured|geo loc name:missing|collection date:missing,Muller glia from mych /  retinas 2 xxx post injury dpi rep2 [5803 ML 8],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",mych /  Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:mych /  Muller glia injured retina|genotype:mych / |treatment:injured,GSM7926869,GSM7926869: Muller glia from mych /  retinas 2 xxx post injury dpi rep2 [5803 ML 8]; Danio rerio; RNA Seq,GSM7926869 r1,GSM7926869,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475451,,loader:fastq load.py,5803-ML-8_CGAGGTGT-CGCCGTTG_S221_R1_001.fastq.gz 5803-ML-8_CGAGGTGT-CGCCGTTG_S221_R2_001.fastq.gz,fastq fastq,45801257486.0,151659793.0,GSM7926869 r1,0:151 1:151,A:12163743496;C:9556065193;G:12415783742;T:11665560316;N:104739,151,151,,,12163743496,9556065193,12415783742,11665560316,104739,SRX22703637,SRS19696112,SRA1761648,University of Michigan,University of Michigan,2,0.82361,0.79223,0.08967,0.0781,0.72614,0.73214,0.51241,0.53445,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29100,SRR27010848,SRX22703636,SRS19696111,SRP475451,PRJNA1047750,Differential expression in Muller glia of injured zebrafish in a mych /  context,GSE249115,Transcriptome Analysis,This experiment studies  retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mych /  Muller glia from injured mych /  fish at 2dpi. Of interest are the WT injury responsive genes  and which injury responsive genes in the WT are differentially expressed in the mych /  fish.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from mych /  retinas 2 xxx post injury dpi rep1 [5803 ML 7],GSM7926868,,source name:mych /  Muller glia injured retina|tissue:mych /  Muller glia injured retina|genotype:mych / |treatment:injured|geo loc name:missing|collection date:missing,Muller glia from mych /  retinas 2 xxx post injury dpi rep1 [5803 ML 7],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",mych /  Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:mych /  Muller glia injured retina|genotype:mych / |treatment:injured,GSM7926868,GSM7926868: Muller glia from mych /  retinas 2 xxx post injury dpi rep1 [5803 ML 7]; Danio rerio; RNA Seq,GSM7926868 r1,GSM7926868,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475451,,loader:fastq load.py,5803-ML-7_ACCTCCGC-AACCTTCA_S220_R1_001.fastq.gz 5803-ML-7_ACCTCCGC-AACCTTCA_S220_R2_001.fastq.gz,fastq fastq,34323078556.0,113652578.0,GSM7926868 r1,0:151 1:151,A:9212407551;C:7253133739;G:9084057760;T:8773400927;N:78579,151,151,,,9212407551,7253133739,9084057760,8773400927,78579,SRX22703636,SRS19696111,SRA1761648,University of Michigan,University of Michigan,2,0.83258,0.79995,0.10182,0.08869,0.7204,0.72506,0.53438,0.53893,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29101,SRR27010849,SRX22703635,SRS19696110,SRP475451,PRJNA1047750,Differential expression in Muller glia of injured zebrafish in a mych /  context,GSE249115,Transcriptome Analysis,This experiment studies  retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mych /  Muller glia from injured mych /  fish at 2dpi. Of interest are the WT injury responsive genes  and which injury responsive genes in the WT are differentially expressed in the mych /  fish.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from WT retinas 2 xxx post injury dpi rep3 [5803 ML 6],GSM7926867,,source name:WT Muller glia injured retina|tissue:WT Muller glia injured retina|genotype:WT|treatment:injured|geo loc name:missing|collection date:missing,Muller glia from WT retinas 2 xxx post injury dpi rep3 [5803 ML 6],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller glia injured retina|genotype:WT|treatment:injured,GSM7926867,GSM7926867: Muller glia from WT retinas 2 xxx post injury dpi rep3 [5803 ML 6]; Danio rerio; RNA Seq,GSM7926867 r1,GSM7926867,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475451,,loader:fastq load.py,5803-ML-6_CTTGAAGG-TAGCGGAG_S219_R1_001.fastq.gz 5803-ML-6_CTTGAAGG-TAGCGGAG_S219_R2_001.fastq.gz,fastq fastq,39633900160.0,131238080.0,GSM7926867 r1,0:151 1:151,A:10574730340;C:8244722619;G:10678580933;T:10135778012;N:88256,151,151,,,10574730340,8244722619,10678580933,10135778012,88256,SRX22703635,SRS19696110,SRA1761648,University of Michigan,University of Michigan,2,0.82908,0.8023,0.08841,0.07628,0.72608,0.73285,0.53006,0.52227,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29102,SRR27010850,SRX22703634,SRS19696109,SRP475451,PRJNA1047750,Differential expression in Muller glia of injured zebrafish in a mych /  context,GSE249115,Transcriptome Analysis,This experiment studies  retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mych /  Muller glia from injured mych /  fish at 2dpi. Of interest are the WT injury responsive genes  and which injury responsive genes in the WT are differentially expressed in the mych /  fish.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from WT retinas 2 xxx post injury dpi rep2 [5803 ML 5],GSM7926866,,source name:WT Muller glia injured retina|tissue:WT Muller glia injured retina|genotype:WT|treatment:injured|geo loc name:missing|collection date:missing,Muller glia from WT retinas 2 xxx post injury dpi rep2 [5803 ML 5],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller glia injured retina|genotype:WT|treatment:injured,GSM7926866,GSM7926866: Muller glia from WT retinas 2 xxx post injury dpi rep2 [5803 ML 5]; Danio rerio; RNA Seq,GSM7926866 r1,GSM7926866,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475451,,loader:fastq load.py,5803-ML-5_TCTCGGAG-CCGTGTGT_S218_R1_001.fastq.gz 5803-ML-5_TCTCGGAG-CCGTGTGT_S218_R2_001.fastq.gz,fastq fastq,42813650610.0,141767055.0,GSM7926866 r1,0:151 1:151,A:11307756303;C:9128581274;G:11491585338;T:10885631489;N:96206,151,151,,,11307756303,9128581274,11491585338,10885631489,96206,SRX22703634,SRS19696109,SRA1761648,University of Michigan,University of Michigan,2,0.84717,0.81641,0.07575,0.06577,0.72456,0.72947,0.51796,0.52376,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29103,SRR27010851,SRX22703633,SRS19696108,SRP475451,PRJNA1047750,Differential expression in Muller glia of injured zebrafish in a mych /  context,GSE249115,Transcriptome Analysis,This experiment studies  retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mych /  Muller glia from injured mych /  fish at 2dpi. Of interest are the WT injury responsive genes  and which injury responsive genes in the WT are differentially expressed in the mych /  fish.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from WT retinas 2 xxx post injury dpi rep1 [5803 ML 4],GSM7926865,,source name:WT Muller glia injured retina|tissue:WT Muller glia injured retina|genotype:WT|treatment:injured|geo loc name:missing|collection date:missing,Muller glia from WT retinas 2 xxx post injury dpi rep1 [5803 ML 4],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller glia injured retina|genotype:WT|treatment:injured,GSM7926865,GSM7926865: Muller glia from WT retinas 2 xxx post injury dpi rep1 [5803 ML 4]; Danio rerio; RNA Seq,GSM7926865 r1,GSM7926865,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475451,,loader:fastq load.py,5803-ML-4_TTACACAC-AACTCCGA_S217_R1_001.fastq.gz 5803-ML-4_TTACACAC-AACTCCGA_S217_R2_001.fastq.gz,fastq fastq,35641811084.0,118019242.0,GSM7926865 r1,0:151 1:151,A:9509123801;C:7547711759;G:9554254572;T:9030640032;N:80920,151,151,,,9509123801,7547711759,9554254572,9030640032,80920,SRX22703633,SRS19696108,SRA1761648,University of Michigan,University of Michigan,2,0.84325,0.81491,0.09102,0.08021,0.71936,0.72368,0.52206,0.51772,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29104,SRR27010852,SRX22703632,SRS19696107,SRP475451,PRJNA1047750,Differential expression in Muller glia of injured zebrafish in a mych /  context,GSE249115,Transcriptome Analysis,This experiment studies  retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mych /  Muller glia from injured mych /  fish at 2dpi. Of interest are the WT injury responsive genes  and which injury responsive genes in the WT are differentially expressed in the mych /  fish.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from uninjured WT retinas rep3 [5803 ML 3],GSM7926864,,source name:WT Muller glia uninjured retina|tissue:WT Muller glia uninjured retina|genotype:WT|treatment:n1|geo loc name:missing|collection date:missing,Muller glia from uninjured WT retinas rep3 [5803 ML 3],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller glia uninjured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller glia uninjured retina|genotype:WT|treatment:n1,GSM7926864,GSM7926864: Muller glia from uninjured WT retinas rep3 [5803 ML 3]; Danio rerio; RNA Seq,GSM7926864 r1,GSM7926864,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475451,,loader:fastq load.py,5803-ML-3_CCTTATGG-GCACGCTT_S216_R2_001.fastq.gz 5803-ML-3_CCTTATGG-GCACGCTT_S216_R1_001.fastq.gz,fastq fastq,44024352302.0,145776001.0,GSM7926864 r1,0:151 1:151,A:12035679681;C:9067037632;G:11325935498;T:11595599635;N:99856,151,151,,,12035679681,9067037632,11325935498,11595599635,99856,SRX22703632,SRS19696107,SRA1761648,University of Michigan,University of Michigan,2,0.83165,0.79093,0.139,0.11939,0.73539,0.74148,0.52839,0.52569,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29105,SRR27010853,SRX22703631,SRS19696106,SRP475451,PRJNA1047750,Differential expression in Muller glia of injured zebrafish in a mych /  context,GSE249115,Transcriptome Analysis,This experiment studies  retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mych /  Muller glia from injured mych /  fish at 2dpi. Of interest are the WT injury responsive genes  and which injury responsive genes in the WT are differentially expressed in the mych /  fish.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from uninjured WT retinas rep2 [5803 ML 2],GSM7926863,,source name:WT Muller glia uninjured retina|tissue:WT Muller glia uninjured retina|genotype:WT|treatment:n1|geo loc name:missing|collection date:missing,Muller glia from uninjured WT retinas rep2 [5803 ML 2],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller glia uninjured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller glia uninjured retina|genotype:WT|treatment:n1,GSM7926863,GSM7926863: Muller glia from uninjured WT retinas rep2 [5803 ML 2]; Danio rerio; RNA Seq,GSM7926863 r1,GSM7926863,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475451,,loader:fastq load.py,5803-ML-2_AGGTCTAT-CCGTGAGA_S215_R1_001.fastq.gz 5803-ML-2_AGGTCTAT-CCGTGAGA_S215_R2_001.fastq.gz,fastq fastq,30776465150.0,101908825.0,GSM7926863 r1,0:151 1:151,A:8433807492;C:6356747786;G:7933043571;T:8052796793;N:69508,151,151,,,8433807492,6356747786,7933043571,8052796793,69508,SRX22703631,SRS19696106,SRA1761648,University of Michigan,University of Michigan,2,0.84084,0.79586,0.14119,0.12143,0.74067,0.74718,0.52859,0.5313,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29106,SRR27010854,SRX22703630,SRS19696105,SRP475451,PRJNA1047750,Differential expression in Muller glia of injured zebrafish in a mych /  context,GSE249115,Transcriptome Analysis,This experiment studies  retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mych /  Muller glia from injured mych /  fish at 2dpi. Of interest are the WT injury responsive genes  and which injury responsive genes in the WT are differentially expressed in the mych /  fish.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from uninjured WT retinas rep1 [5803 ML 1 ],GSM7926862,,source name:WT Muller glia uninjured retina|tissue:WT Muller glia uninjured retina|genotype:WT|treatment:n1|geo loc name:missing|collection date:missing,Muller glia from uninjured WT retinas rep1 [5803 ML 1 ],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller glia uninjured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller glia uninjured retina|genotype:WT|treatment:n1,GSM7926862,GSM7926862: Muller glia from uninjured WT retinas rep1 [5803 ML 1 ]; Danio rerio; RNA Seq,GSM7926862 r1,GSM7926862,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475451,,loader:fastq load.py,5803-ML-1_AAGGACCG-GACACAAG_S214_R1_001.fastq.gz 5803-ML-1_AAGGACCG-GACACAAG_S214_R2_001.fastq.gz,fastq fastq,35814764672.0,118591936.0,GSM7926862 r1,0:151 1:151,A:10118857494;C:7312994344;G:8767136259;T:9615695615;N:80960,151,151,,,10118857494,7312994344,8767136259,9615695615,80960,SRX22703630,SRS19696105,SRA1761648,University of Michigan,University of Michigan,2,0.84915,0.79824,0.17335,0.14475,0.72103,0.73097,0.51291,0.4893,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
30572,SRR27848813,SRX23511754,SRS20362222,SRP487850,PRJNA1072679,Oxidative stress  altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However  excessive ROS can lead to oxidative stress  inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM  an X linked chorioretinal dystrophy which predominantly affects the photoreceptors  retinal pigment epithelium RPE and choroid. In this study  we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration  upregulation of oxidative  ER stress and apoptosis markers  and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay  but post overexpression of human PFKM  it partially rescued the retinal phenotype and glucose uptake  but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy  caused by mutations in the CHM gene. It is a progressive condition leading to  complete blindness. We are working on a chm zebrafish model  which shows a widespread severe degenerative phenotype  with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Wildtype 7,GSM8061015,,source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing,Wildtype 7,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11  both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Wildtype,GSM8061015,GSM8061015: Wildtype 7; Danio rerio; RNA Seq,GSM8061015 r1,GSM8061015,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,WT7_1.fq.gz WT7_2.fq.gz,fastq fastq,16387213200.0,54624044.0,GSM8061015 r1,0:150 1:150,A:4787207224;C:3312386758;G:3384738324;T:4902574775;N:306119,150,150,,,4787207224,3312386758,3384738324,4902574775,306119,SRX23511754,SRS20362222,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.92431,0.91825,0.16903,0.16976,0.74067,0.75189,0.50167,0.50261,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System
30573,SRR27848814,SRX23511753,SRS20362221,SRP487850,PRJNA1072679,Oxidative stress  altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However  excessive ROS can lead to oxidative stress  inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM  an X linked chorioretinal dystrophy which predominantly affects the photoreceptors  retinal pigment epithelium RPE and choroid. In this study  we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration  upregulation of oxidative  ER stress and apoptosis markers  and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay  but post overexpression of human PFKM  it partially rescued the retinal phenotype and glucose uptake  but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy  caused by mutations in the CHM gene. It is a progressive condition leading to  complete blindness. We are working on a chm zebrafish model  which shows a widespread severe degenerative phenotype  with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Wildtype 6,GSM8061014,,source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing,Wildtype 6,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11  both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Wildtype,GSM8061014,GSM8061014: Wildtype 6; Danio rerio; RNA Seq,GSM8061014 r1,GSM8061014,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,WT6_1.fq.gz WT6_2.fq.gz,fastq fastq,19114278900.0,63714263.0,GSM8061014 r1,0:150 1:150,A:5885874877;C:3513555230;G:3610119151;T:6104379853;N:349789,150,150,,,5885874877,3513555230,3610119151,6104379853,349789,SRX23511753,SRS20362221,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.88104,0.87237,0.33066,0.33508,0.7357,0.7499,0.52706,0.51369,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System
30574,SRR27848815,SRX23511752,SRS20362220,SRP487850,PRJNA1072679,Oxidative stress  altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However  excessive ROS can lead to oxidative stress  inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM  an X linked chorioretinal dystrophy which predominantly affects the photoreceptors  retinal pigment epithelium RPE and choroid. In this study  we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration  upregulation of oxidative  ER stress and apoptosis markers  and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay  but post overexpression of human PFKM  it partially rescued the retinal phenotype and glucose uptake  but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy  caused by mutations in the CHM gene. It is a progressive condition leading to  complete blindness. We are working on a chm zebrafish model  which shows a widespread severe degenerative phenotype  with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Wildtype 5,GSM8061013,,source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing,Wildtype 5,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11  both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Wildtype,GSM8061013,GSM8061013: Wildtype 5; Danio rerio; RNA Seq,GSM8061013 r1,GSM8061013,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,WT5_2.fq.gz WT5_1.fq.gz,fastq fastq,16120305900.0,53734353.0,GSM8061013 r1,0:150 1:150,A:4774586081;C:3152393582;G:3245217813;T:4947808687;N:299737,150,150,,,4774586081,3152393582,3245217813,4947808687,299737,SRX23511752,SRS20362220,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.90351,0.89372,0.19598,0.19188,0.74468,0.76037,0.49643,0.5012,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System
30575,SRR27848816,SRX23511751,SRS20362219,SRP487850,PRJNA1072679,Oxidative stress  altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However  excessive ROS can lead to oxidative stress  inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM  an X linked chorioretinal dystrophy which predominantly affects the photoreceptors  retinal pigment epithelium RPE and choroid. In this study  we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration  upregulation of oxidative  ER stress and apoptosis markers  and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay  but post overexpression of human PFKM  it partially rescued the retinal phenotype and glucose uptake  but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy  caused by mutations in the CHM gene. It is a progressive condition leading to  complete blindness. We are working on a chm zebrafish model  which shows a widespread severe degenerative phenotype  with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Wildtype 4,GSM8061012,,source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing,Wildtype 4,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11  both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Wildtype,GSM8061012,GSM8061012: Wildtype 4; Danio rerio; RNA Seq,GSM8061012 r1,GSM8061012,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,WT4_1.fq.gz WT4_2.fq.gz,fastq fastq,15545813700.0,51819379.0,GSM8061012 r1,0:150 1:150,A:4735339999;C:2883223993;G:2979819364;T:4947148649;N:281695,150,150,,,4735339999,2883223993,2979819364,4947148649,281695,SRX23511751,SRS20362219,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.88431,0.87409,0.2472,0.24596,0.74675,0.76534,0.50472,0.51348,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System
30576,SRR27848817,SRX23511750,SRS20362218,SRP487850,PRJNA1072679,Oxidative stress  altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However  excessive ROS can lead to oxidative stress  inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM  an X linked chorioretinal dystrophy which predominantly affects the photoreceptors  retinal pigment epithelium RPE and choroid. In this study  we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration  upregulation of oxidative  ER stress and apoptosis markers  and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay  but post overexpression of human PFKM  it partially rescued the retinal phenotype and glucose uptake  but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy  caused by mutations in the CHM gene. It is a progressive condition leading to  complete blindness. We are working on a chm zebrafish model  which shows a widespread severe degenerative phenotype  with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Wildtype 3,GSM8061011,,source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing,Wildtype 3,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11  both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Wildtype,GSM8061011,GSM8061011: Wildtype 3; Danio rerio; RNA Seq,GSM8061011 r1,GSM8061011,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,WT3_1.fq.gz WT3_2.fq.gz,fastq fastq,17883593700.0,59611979.0,GSM8061011 r1,0:150 1:150,A:5305029339;C:3503937995;G:3594774195;T:5479523425;N:328746,150,150,,,5305029339,3503937995,3594774195,5479523425,328746,SRX23511750,SRS20362218,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.90376,0.89786,0.22127,0.22019,0.72941,0.74257,0.49283,0.4977,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System
30577,SRR27848818,SRX23511749,SRS20362217,SRP487850,PRJNA1072679,Oxidative stress  altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However  excessive ROS can lead to oxidative stress  inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM  an X linked chorioretinal dystrophy which predominantly affects the photoreceptors  retinal pigment epithelium RPE and choroid. In this study  we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration  upregulation of oxidative  ER stress and apoptosis markers  and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay  but post overexpression of human PFKM  it partially rescued the retinal phenotype and glucose uptake  but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy  caused by mutations in the CHM gene. It is a progressive condition leading to  complete blindness. We are working on a chm zebrafish model  which shows a widespread severe degenerative phenotype  with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Wildtype 2,GSM8061010,,source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing,Wildtype 2,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11  both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Wildtype,GSM8061010,GSM8061010: Wildtype 2; Danio rerio; RNA Seq,GSM8061010 r1,GSM8061010,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,WT2_1.fq.gz WT2_2.fq.gz,fastq fastq,15921002400.0,53070008.0,GSM8061010 r1,0:150 1:150,A:4801739158;C:2898179014;G:3037454009;T:5183338180;N:292039,150,150,,,4801739158,2898179014,3037454009,5183338180,292039,SRX23511749,SRS20362217,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.88935,0.87616,0.22376,0.2085,0.75367,0.78123,0.53443,0.51122,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System
30578,SRR27848819,SRX23511748,SRS20362216,SRP487850,PRJNA1072679,Oxidative stress  altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However  excessive ROS can lead to oxidative stress  inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM  an X linked chorioretinal dystrophy which predominantly affects the photoreceptors  retinal pigment epithelium RPE and choroid. In this study  we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration  upregulation of oxidative  ER stress and apoptosis markers  and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay  but post overexpression of human PFKM  it partially rescued the retinal phenotype and glucose uptake  but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy  caused by mutations in the CHM gene. It is a progressive condition leading to  complete blindness. We are working on a chm zebrafish model  which shows a widespread severe degenerative phenotype  with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Wildtype 1,GSM8061009,,source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing,Wildtype 1,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11  both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Wildtype,GSM8061009,GSM8061009: Wildtype 1; Danio rerio; RNA Seq,GSM8061009 r1,GSM8061009,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,WT1_1.fq.gz WT1_2.fq.gz,fastq fastq,15664926900.0,52216423.0,GSM8061009 r1,0:150 1:150,A:4654413024;C:3082161368;G:3150203371;T:4777859952;N:289185,150,150,,,4654413024,3082161368,3150203371,4777859952,289185,SRX23511748,SRS20362216,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.9012,0.89646,0.22096,0.21863,0.73507,0.7475,0.4816,0.4726,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System
30579,SRR27848820,SRX23511747,SRS20362215,SRP487850,PRJNA1072679,Oxidative stress  altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However  excessive ROS can lead to oxidative stress  inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM  an X linked chorioretinal dystrophy which predominantly affects the photoreceptors  retinal pigment epithelium RPE and choroid. In this study  we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration  upregulation of oxidative  ER stress and apoptosis markers  and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay  but post overexpression of human PFKM  it partially rescued the retinal phenotype and glucose uptake  but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy  caused by mutations in the CHM gene. It is a progressive condition leading to  complete blindness. We are working on a chm zebrafish model  which shows a widespread severe degenerative phenotype  with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Choroideremia 7,GSM8061008,,source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing,Choroideremia 7,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11  both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Choroideremia,GSM8061008,GSM8061008: Choroideremia 7; Danio rerio; RNA Seq,GSM8061008 r1,GSM8061008,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,CHM7_2.fq.gz CHM7_1.fq.gz,fastq fastq,16991281200.0,56637604.0,GSM8061008 r1,0:150 1:150,A:4896856485;C:3497447652;G:3598783228;T:4998138764;N:55071,150,150,,,4896856485,3497447652,3598783228,4998138764,55071,SRX23511747,SRS20362215,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.926,0.92518,0.16779,0.16551,0.72393,0.73513,0.51723,0.51214,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System
30580,SRR27848821,SRX23511746,SRS20362214,SRP487850,PRJNA1072679,Oxidative stress  altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However  excessive ROS can lead to oxidative stress  inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM  an X linked chorioretinal dystrophy which predominantly affects the photoreceptors  retinal pigment epithelium RPE and choroid. In this study  we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration  upregulation of oxidative  ER stress and apoptosis markers  and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay  but post overexpression of human PFKM  it partially rescued the retinal phenotype and glucose uptake  but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy  caused by mutations in the CHM gene. It is a progressive condition leading to  complete blindness. We are working on a chm zebrafish model  which shows a widespread severe degenerative phenotype  with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Choroideremia 6,GSM8061007,,source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing,Choroideremia 6,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11  both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Choroideremia,GSM8061007,GSM8061007: Choroideremia 6; Danio rerio; RNA Seq,GSM8061007 r1,GSM8061007,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,CHM6_1.fq.gz CHM6_2.fq.gz,fastq fastq,18881901900.0,62939673.0,GSM8061007 r1,0:150 1:150,A:5796692721;C:3348140904;G:3547934333;T:6189072751;N:61191,150,150,,,5796692721,3348140904,3547934333,6189072751,61191,SRX23511746,SRS20362214,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.86869,0.86484,0.26053,0.2569,0.75057,0.77705,0.66121,0.65975,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System
30581,SRR27848822,SRX23511745,SRS20362213,SRP487850,PRJNA1072679,Oxidative stress  altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However  excessive ROS can lead to oxidative stress  inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM  an X linked chorioretinal dystrophy which predominantly affects the photoreceptors  retinal pigment epithelium RPE and choroid. In this study  we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration  upregulation of oxidative  ER stress and apoptosis markers  and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay  but post overexpression of human PFKM  it partially rescued the retinal phenotype and glucose uptake  but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy  caused by mutations in the CHM gene. It is a progressive condition leading to  complete blindness. We are working on a chm zebrafish model  which shows a widespread severe degenerative phenotype  with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Choroideremia 5,GSM8061006,,source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing,Choroideremia 5,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11  both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Choroideremia,GSM8061006,GSM8061006: Choroideremia 5; Danio rerio; RNA Seq,GSM8061006 r1,GSM8061006,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,CHM5_2.fq.gz CHM5_1.fq.gz,fastq fastq,17802156900.0,59340523.0,GSM8061006 r1,0:150 1:150,A:5198674613;C:3599354426;G:3698229931;T:5305840019;N:57911,150,150,,,5198674613,3599354426,3698229931,5305840019,57911,SRX23511745,SRS20362213,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.9109,0.91251,0.18901,0.18793,0.72354,0.73456,0.51839,0.52348,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System
30582,SRR27848823,SRX23511744,SRS20362212,SRP487850,PRJNA1072679,Oxidative stress  altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However  excessive ROS can lead to oxidative stress  inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM  an X linked chorioretinal dystrophy which predominantly affects the photoreceptors  retinal pigment epithelium RPE and choroid. In this study  we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration  upregulation of oxidative  ER stress and apoptosis markers  and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay  but post overexpression of human PFKM  it partially rescued the retinal phenotype and glucose uptake  but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy  caused by mutations in the CHM gene. It is a progressive condition leading to  complete blindness. We are working on a chm zebrafish model  which shows a widespread severe degenerative phenotype  with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Choroideremia 4,GSM8061005,,source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing,Choroideremia 4,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11  both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Choroideremia,GSM8061005,GSM8061005: Choroideremia 4; Danio rerio; RNA Seq,GSM8061005 r1,GSM8061005,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,CHM4_2.fq.gz CHM4_1.fq.gz,fastq fastq,15944831400.0,53149438.0,GSM8061005 r1,0:150 1:150,A:4833633886;C:2870981386;G:3055307522;T:5184819306;N:89300,150,150,,,4833633886,2870981386,3055307522,5184819306,89300,SRX23511744,SRS20362212,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.88929,0.88364,0.25277,0.24996,0.75317,0.77826,0.64914,0.65907,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System
30583,SRR27848824,SRX23511743,SRS20362211,SRP487850,PRJNA1072679,Oxidative stress  altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However  excessive ROS can lead to oxidative stress  inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM  an X linked chorioretinal dystrophy which predominantly affects the photoreceptors  retinal pigment epithelium RPE and choroid. In this study  we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration  upregulation of oxidative  ER stress and apoptosis markers  and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay  but post overexpression of human PFKM  it partially rescued the retinal phenotype and glucose uptake  but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy  caused by mutations in the CHM gene. It is a progressive condition leading to  complete blindness. We are working on a chm zebrafish model  which shows a widespread severe degenerative phenotype  with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Choroideremia 3,GSM8061004,,source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing,Choroideremia 3,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11  both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Choroideremia,GSM8061004,GSM8061004: Choroideremia 3; Danio rerio; RNA Seq,GSM8061004 r1,GSM8061004,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,CHM3_1.fq.gz CHM3_2.fq.gz,fastq fastq,16028608800.0,53428696.0,GSM8061004 r1,0:150 1:150,A:4842495383;C:2966448486;G:3084331699;T:5135033798;N:299434,150,150,,,4842495383,2966448486,3084331699,5135033798,299434,SRX23511743,SRS20362211,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.89747,0.88445,0.23706,0.23597,0.72904,0.75187,0.5514,0.45471,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System
30584,SRR27848825,SRX23511742,SRS20362210,SRP487850,PRJNA1072679,Oxidative stress  altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However  excessive ROS can lead to oxidative stress  inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM  an X linked chorioretinal dystrophy which predominantly affects the photoreceptors  retinal pigment epithelium RPE and choroid. In this study  we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration  upregulation of oxidative  ER stress and apoptosis markers  and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay  but post overexpression of human PFKM  it partially rescued the retinal phenotype and glucose uptake  but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy  caused by mutations in the CHM gene. It is a progressive condition leading to  complete blindness. We are working on a chm zebrafish model  which shows a widespread severe degenerative phenotype  with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Choroideremia 2,GSM8061003,,source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing,Choroideremia 2,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11  both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Choroideremia,GSM8061003,GSM8061003: Choroideremia 2; Danio rerio; RNA Seq,GSM8061003 r1,GSM8061003,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,CHM2_1.fq.gz CHM2_2.fq.gz,fastq fastq,14968884300.0,49896281.0,GSM8061003 r1,0:150 1:150,A:4575866591;C:2606132581;G:2819446784;T:4967389772;N:48572,150,150,,,4575866591,2606132581,2819446784,4967389772,48572,SRX23511742,SRS20362210,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.88022,0.87326,0.29312,0.29812,0.7335,0.76228,0.5854,0.57614,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System
30585,SRR27848826,SRX23511741,SRS20362209,SRP487850,PRJNA1072679,Oxidative stress  altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However  excessive ROS can lead to oxidative stress  inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM  an X linked chorioretinal dystrophy which predominantly affects the photoreceptors  retinal pigment epithelium RPE and choroid. In this study  we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration  upregulation of oxidative  ER stress and apoptosis markers  and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay  but post overexpression of human PFKM  it partially rescued the retinal phenotype and glucose uptake  but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy  caused by mutations in the CHM gene. It is a progressive condition leading to  complete blindness. We are working on a chm zebrafish model  which shows a widespread severe degenerative phenotype  with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Choroideremia 1,GSM8061002,,source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing,Choroideremia 1,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11  both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Choroideremia,GSM8061002,GSM8061002: Choroideremia 1; Danio rerio; RNA Seq,GSM8061002 r1,GSM8061002,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,CHM1_2.fq.gz CHM1_1.fq.gz,fastq fastq,15862639500.0,52875465.0,GSM8061002 r1,0:150 1:150,A:4812544148;C:2881706406;G:3014671171;T:5153419977;N:297798,150,150,,,4812544148,2881706406,3014671171,5153419977,297798,SRX23511741,SRS20362209,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.89157,0.87804,0.24616,0.24284,0.73884,0.76232,0.58251,0.58918,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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